Having obtained a deep grounding in Talmud, Rabbi Hutner was sent to join an extension of the Slabodka yeshiva in Hebron. He studied there until 1929, narrowly escaping the 1929 Hebron massacre because he was away for the weekend. It was during his stay in the British Mandate of Palestine that he became a disciple of Rabbi Abraham Isaac Kook, the first chief rabbi of Palestine (as it was then known.) The philosophical and mystical mind-set of both men, made them kindred spirits. Like Rabbi Kook, the young Rabbi Hutner eventually developed a warm welcoming posture towards non-religious Jews who were seeking to become more religious. They viewed things in the context of the end of the Jewish exile, golus (galut), with the imminent coming of the messianic era.
In later years, when Rabbi Kook's name became entrenched with the Mizrachi, part of the Religious Zionist Movement, Rabbi Hutner, as an eventual member of the non-Zionist Haredi Agudath Israel of America's Moetzes Gedolei HaTorah ("Council of Torah Sages"), sought to decrease his former association with Kook, even though he maintained cordial relations with Rabbi Kook's son and heir Rabbi Zvi Yehuda Kook and others such as Rabbi Moshe Tzvi Neriah. Rabbi Hutner's students recount that on Sukkot Rabbi Hutner would hang a portrait of Rabbi Kook in his sukkah. When the matter of conscripting religious girls (giyus banot) into the Israel Defense Forces became a controversial matter after the founding of the State of Israel in 1948, the photo of Rabbi Kook was removed and replaced with one of Rabbi Avrohom Yeshaya Karelitz who ruled that Jewish females are forbidden to serve in the IDF. Finally, when Rabbi Hutner composed and published his work Pachad Yitzchok there is absolutely no overt reference to any of Rabbi Kook's own extensive works (although Rabbi Kook's notions and motifs permeate Rabbi Hutner's work to those familiar with both rabbis' writings.) However, there are a select few of Rabbi Hutner's early students who recall some of Rabbi Hutner's lengthy comments to them regarding Rabbi Kook, but none of them have ever written or said anything about what was said to them in a public forum. It has remained for the Religious Zionist teacher, Rabbi Moshe Zvi Neriah to republish the approbation that Rabbi Kook had written and some correspondence between Rabbis Kook and Hutner about it.
After the pogrom in Hebron in 1929, Rabbi Hutner spent some years as a wandering scholar. First, he returned to Warsaw, from there going to study philosophy at the University of Berlin, but not for degree purposes; he was not interested in degrees or the jobs they could offer, but only in the actual material that the university taught him. During this period he wrote Torat HaNazir, on the laws of the Nazarite. He spent time familiarizing himself with the intellectual milieu of Germany.
He befriended two other future rabbinical leaders studying secular philosophy in Berlin: Rabbi Joseph B. Soloveitchik, who was to become rosh yeshiva at Yeshiva University in New York City, and Rabbi Menachem Mendel Schneerson who would become rebbe of Chabad-Lubavitch in Brooklyn. The three were to retain close and cordial personal relations throughout their lives, even though each differed from the other radically in Torah weltanschauung (hashkafa). Nevertheless, each developed a unique bridge and synthesis between the Eastern European world-view connecting it with a Westernized way of thinking. This was a key factor enabling them to serve successfully as spiritual leaders in the United States of America.
After marrying his American-born wife, Masha Lipshitz, in Warsaw, Poland, in 1932, the couple spent about a year in Palestine where Rabbi Hutner completed his research and writing of his Kovetz Ha'aros on Hillel ben Eliakim's commentary on midrash sifra. He visited Europe in 1934 to collate manuscripts of Hillel ben Eliakim's commentary.
By 1935 the couple had emigrated to Brooklyn, New York where Rabbi Hutner pursued his private studies, initially not actively seeking a formal position. However, he soon joined the faculty of the Yeshiva Rabbi Jacob Joseph (RJJ) and sometime between 1935–1936 was appointed first as a teacher then as principal of the newly established high school division of the Yeshiva Rabbi Chaim Berlin known as Mesivta Yeshiva Rabbi Chaim Berlin. The yeshiva had been the oldest elementary yeshiva in Brooklyn since 1904. During 1939 and 1940 he established the yeshiva's post-high school beth midrash division and became the senior rosh yeshivah of the entire Yeshiva Rabbi Chaim Berlin. In this effort he also received the help of Rabbi Shraga Feivel Mendlowitz who headed Brooklyn's largest and more established Yeshiva Torah Vodaas. Under Rabbi Hutner's charismatic leadership, Yeshiva Rabbi Chaim Berlin grew from relative obscurity to prominence, and with it grew his reputation in the world of Torah scholarship.
He was able to construct an intense curriculum and an environment that produced young Talmudic scholars who were viewed as being in the same league as their compatriots in Eastern Europe. By 1940 he had established a post-high school yeshiva, beth midrash with hundreds of students.
He viewed secular studies as essential in learning a profession for people to support themselves by eventually going to college and becoming professionals. Together with the dean of the Yeshiva Torah Vodaas, Shraga Feivel Mendlowitz a charter to set up a combined yeshiva and college was obtained from the New York State Board of Regents. However, this plan was abandoned upon the insistence of Rabbi Aaron Kotler the anti-secular leader of the Lakewood yeshiva (Beth Medrash Gevoha), which would become the largest yeshiva of its kind in the United States, who wielded great influence and rabbinical power. In this and other matters Rabbi Hutner acquiesced to Rabbi Kotler.
Hutner however maintained his relatively liberal policy during his tenure at the helm of his own Yeshiva Rabbi Chaim Berlin, allowing students to combine their day's learning in yeshiva together with attending college, mainly at Brooklyn College and later at Touro College in late afternoons and evenings. He would take great pride in the secular accomplishments of his students insofar as they would fit into his vision of a material world governed by the principles of a spiritual Torah way of life. One of his closest disciples is the renowned economist, Rabbi Israel Kirzner who edited Hutner's written works, Pachad Yitzchok. Many of Hutner's disciples went about quietly obtaining doctorates often with his blessings and guidance, including his daughter Rebbetzin Dr. Bruria Hutner David (philosophy). The list includes Rabbis Shlomo Teichman (mathematics) founder and dean of Bais Yaakov Academy, Shlomo Braunstein (statistics) rosh yeshiva and principal, Shlomo Ribner (psychology) psychologist and rosh yeshiva, Moshe Homnick (psychology), Ahron Soloveichik (law) rosh yeshiva, Aharon Lichtenstein (literature) rosh yeshiva, Dr Abraham J. Tannenbaum (education), Joseph Thurm (information technology), Naftoli Langsam (education), Yedidya Langsam (biology), Chaim Feuerman (education). Many alumni of his yeshiva have attained success as attorneys, accountants, doctors, and in information technology.
Rabbi Hutner was well versed in many intellectual areas, even studying and refuting secular and non-traditional Jewish scholarship. There was an interesting episode where a student made a remark about some religious issue. Rabbi Hutner allegedly slapped him and said, "You read that in Heschel!"
His daughter and only child, Rebbetzin Bruria Hutner David, obtained her Ph.D. at Columbia University in the department of philosophy as a student of Salo Baron. She subsequently founded and became the dean of a major seminary for Jewish women in Jerusalem known as Beth Jacob of Jerusalem (BJJ) that caters to young women from Haredi families in the United States. Her dissertation discussed the dual role of Rabbi Zvi Hirsch Chajes as both a traditionalist and maskil ("follower of the enlightenment"). Some have noted the remarkable parallels between her own father and Rabbi Chajes, the subject of her dissertation.
Rabbi Hutner appointed Slabodka yeshiva educated Rabbi Avigdor Miller as the Mashgiach ruchani ("spiritual mentor and supervisor") of the yeshiva. After the yeshiva relocated to Far Rockaway, New York in the 1960s, Rabbi Miller resigned from his position due to the difficulties a daily commute from Brooklyn entailed.
Rabbi Hutner developed a style of celebrating Shabbat and the Holy Days, Yom Tov, by giving a kind of talk called a maamer. It was a combination of Talmudic discourse, Hasidic celebration (tish), philosophic lecture, group singing, and when possible, like on Purim, a ten piece band was brought in as accompaniment. Many times there was singing and dancing all night. All of this, together with the respect to his authority that he demanded, induced in his students obedience and something of a "heightened consciousness" that passed into their lives making them into literal hasidim ("devotees") of their rosh yeshiva, who encouraged this by eventually personally donning Hasidic garb, (begadim) and acting outwardly like a synthesis between a rosh yeshiva and a rebbe and instructed some of his students to do like-wise.
His methodology and style was complex and controversial and ultimately difficult to pigeonhole, although intellectually he placed great emphasis on penetrating Talmudic study and analysis, emotionally he veered towards the Hasidic-style, more than his Lithuanian-style colleagues reared as "mitnagdim" could tolerate. Ironically, Rabbi Hutner became a fierce critic of Lubavitch and the idolization of Rabbi Menachem Schneerson. Yet both men referred to their discourses as maamarim. He also forbade his students from attending any lectures given by Rabbi Joseph B. Soloveitchik at the same time that he appointed Rabbi Soloveitchik's younger brother, whom he had tutored in Warsaw, Rabbi Ahron Soloveichik (later to head his own yeshiva in Skokie near Chicago, Illinois) as head of his own Yeshiva Rabbi Chaim Berlin. Rabbi Ahron Soloveichik completed a Doctorate in law at New York University at the same time that he lectured in Rabbi Hutner's Yeshiva Rabbi Chaim Berlin.
In the 1950s, he established a school for post-graduate married scholars to continue their in-depth Talmudical studies. This was a kollel, (a post graduate division), the Kollel Gur Aryeh, one of the first of its kind in America. Many of his students became prominent educational, outreach, and pulpit rabbis. He stayed in touch with them and was intimately involved in major communal policy decision-making as he worked through his network of students in positions of leadership, and won over to his cause people who came to meet with him.
He published what is considered his magnum opus which he named Pachad Yitzchok, ("Fear [of] Isaac", meaning the God whom Isaac feared). He called his outlook Hilchot Deot Vechovot Halevavot, ("Laws [of] 'Ideas' and 'Duties [of the] Heart'") and wrote in a poetic modern-style Hebrew reminiscent of his original mentor's style, Rabbi Abraham Isaac Kook, even though almost all of Rabbi Hutner's original lectures were delivered in Yiddish.
The core of his synthesis of different schools of Jewish thought was rooted in his deep studies of the teachings of Rabbi Judah Loew ben Bezalel (1525–1609) a scholar and mystic known as the Maharal of Prague. It is commonly accepted that Rabbi Hutner "opened up" and "popularized" the writings and ideas of the Maharal. Another pillar of Rabbi Hutner's thought system were the works of the Vilna Gaon, Rabbi Elijah, (1720–1797) and of Rabbi Moshe Chaim Luzzatto (1707–1746). He would only allude in the most general ways to other great mystics, in Hebrew mekubalim, such as the Baal Shem Tov (founder of Hasidism), the great mystic known as the Ari who lived in the late Middle Ages, the founder of Lubavitch Hasidism, the Baal HaTanya Shneur Zalman of Liadi, Rabbi Mordechai Yosef Leiner of Izbitz and many other great Hasidic masters as well as to the great works of Kabbalah such as the Zohar.
He was the mentor of some famous as well as controversial figures in modern Jewish outreach to non-Orthodox Jews, such as Rabbi Shlomo Carlebach, who became the "Singing Rabbi", and Rabbi David Weiss Halivni, who became a prominent scholar at the Jewish Theological Seminary of Conservative Judaism. However, it should be noted that both these personalities split with Rabbi Hutner and moved off into what they ultimately became. Another was a cousin to the earlier Shlomo Carlebach, who also was called Rabbi Shlomo Carlebach, who was appointed as the mashgiach ruchani ("spiritual supervisor") at the Yeshiva Chaim Berlin, but who split with Rabbi Hutner on policy matters in the 1970s. All three were Holocaust survivors who Rabbi Hutner took upon himself to raise as his own "sons" together with others in similar circumstances.
In the early forties Rabbi Hutner asked a friend from Slabodka, Rabbi Saul Lieberman to become a dean-Talmudical lecturer in Yeshiva Rabbi Chaim Berlin. Lieberman instead accepted an offer from the Jewish Theological Seminary, the seminary of Conservative Judaism.
Rabbi Hutner had a number of disagreements with some of the religious scholars who taught in his Yeshiva. These disputes were usually not over ideology, but about positions in the school. Rabbi Hutner attempted (and did in many cases) ease out the older rabbis who were his contemporaries in favor of his disciples. Rabbi Prusskin (a first cousin to his wife), Rabbi Goldstone, Rabbi Shurkin, Rabbi Snow, Rabbi Avrohom Asher Zimmerman and others are among them.
He did initiate a number of changes in Yeshiva Rabbi Chaim Berlin that differed greatly from the mussar yeshiva practice in Slabodka. He abolished the half hour learning session in mussar ("ethics") and replaced it with one of ten or fifteen minutes. He changed the traditional mussar lecture to a maamar utilizing Maharal instead of the classical mussar approach to Torah study.
His students included Rabbis: Yonasan David (his son-in-law) and Aharon Schechter, his successors as Rosh Yeshivas of Yeshiva Rabbi Chaim Berlin; Aharon Lichtenstein, son-in-law of Rabbi Joseph B. Soloveitchik and Rosh Yeshiva of Yeshivat Har Etzion in Israel; Menachem Mendel Blachman, head of the overseas program of Yeshivat Kerem B'Yavneh; Pinchas Stolper of the Orthodox Union and founder of NCSY who followed Rabbi Hutner's guidelines in setting up this youth outreach movement; Avrohom Davis, founder of the Metzudah religious books series; Shlomo Freifeld who set up the one of the first full-time yeshivas for Baal teshuva students in the world, and who personally maintained an open relationship with Lubavitch; Joshua Fishman, leader and executive Vice President of Torah Umesorah the National Society for Hebrew Day Schools; Avrohom Kleinkaufman, a lecturer in Yeshiva of Far Rockaway and translator of the Genesis and Exodus volumes of the Metzuda Bible Commentary of Rabbi Solomon and the Kol Sasson Sephardic Siddurim and Machzorim; Yaakov Perlow, the Novominsker Rebbe of Boro Park; Meir Bilitzky, senior rabbi of Young Israel of New Hyde Park; Noah Weinberg founder and head of the Baal teshuva outreach conglomerate called Aish Hatorah and his brother Yaakov Weinberg of Ner Israel Yeshiva in Baltimore; Yosef Katzenstein of Copenhagen, author of Kol Chayil and Lema'an Achai'; Dovid Cohen, rabbi of Congregation Gvul Yaabetz and an author of a number of books on Jewish theology.
In the late 1960s he began to visit Israel again planning to build a new yeshiva there. In 1970 he, together with his wife, daughter and son-in-law Rabbi Yonasan David, were captured by the PFLP Palestinian terrorist organization, who were in turn attacked by King Hussein's army in Amman, Jordan where the hostages found themselves after being let off the planes that were hijacked. Many Jews prayed fervently for his safe release. Indeed, Rabbi Moshe Feinstein and Agudath Israel of America, Rabbi Joseph B. Soloveitchik, and Rabbi Menachem Schneerson pulled every political string they possessed to ensure his safety.
In spite of this experience, Rabbi Hutner continued his efforts to build his yeshiva in Israel. Eventually it was set up and named Yeshiva Pachad Yitzchok based on his life's work, in Har Nof, Jerusalem. He died in 1980 and is buried in Jerusalem.