For forty-two years (1880-1922), Hirsch served as the rabbi of Chicago Sinai Congregation, one of the oldest synagogues in the midwest. At this post, he became well-known for an emphasis on social justice. From Chicago Sinai's pulpit, he delivered rousing sermons on the social ills of the day and many Chicagoans, Jew and gentile alike, were in attendance.
He was an influential exponent of advanced thought and Reform Judaism. He edited Der Zeitgeist (Milwaukee) (1880–82) and the Reform Advocate (1891–1923). He also edited the Department of the Bible of the Jewish Encyclopedia.
Hirsch is the namesake of the Emil G. Hirsch Metropolitan High School of Communications (Hirsch Metro), located in the South Shore neighborhood of Chicago. In keeping with his interest in education, Hirsch advised a wealthy congregant, Julius Rosenwald of Sears, Roebuck & Co., to use part of his wealth to help build public schools which black students could attend in the segregated south. The school building program was one of the largest programs, but not the only, administered by the Rosenwald Fund.