Hinckley's presidency was noted for the building of new temples, including a reconstruction of the historic Nauvoo Illinois Temple, the building of the 20,000 seat Conference Center, the issuance of the Proclamation on the Family, and the creation of the church's Perpetual Education Fund. Hinckley dedicated more LDS Church temples than anyone else, dedicating more than half of the current temples. At the time of Hinckley's death, approximately one-third of the church's membership had joined the church under Hinckley's leadership. As president of the church, Hinckley was also chairman of the Church Board of Education and Board of Trustees that governs the Church Educational System.
In the early 1950s, Hinckley was part of a committee that considered how to present the temple ordinances at the Swiss Temple. The concern was how this could be done when there would be a need to provide them in at least ten languages; the concern was eventually solved through the use of a film version of the Endowment. Hinckley's background in journalism and public relations prepared him well to preside over the church during a time when it has received increasing media coverage.
The Mark Hofmann document forgeries, bombings, and investigation occurred during this time. Several books describe the arrangements for acquiring supposed historical documents for the church by Hinckley and others. For example, the Stowell forgery implicating Joseph Smith in gold digging was purchased for $15,000 by Hinckley on behalf of the church from Hofmann on the promise of confidentiality. However, two years later Hofmann leaked its existence to the “Mormon intellectual underground.” Upon inquiry, church Spokesman Jerry Cahill denied that the church possessed the document. Hinckley corrected Cahill and released the letter to scholars for study. The document was later found to be a forgery.
After Kimball's death in November 1985, then-former President of the Quorum of the Twelve Apostles Ezra Taft Benson became president of the church and named Hinckley his first counselor. Fellow apostle Thomas S. Monson was named second counselor, and, for a while, all three members of the First Presidency were able to perform their duties. In the early 1990s, however, Benson developed serious health problems that removed him from public view, and Hinckley again carried out many of the duties of the president of the church until Benson died in 1994. After Benson’s death, Howard W. Hunter became President and retained Hinckley and Monson as counselors in the First Presidency. At the same time, Hinckley became President of the Quorum of the Twelve Apostles by virtue of seniority.
When Hunter died after a presidency of only nine months, Hinckley succeeded to the presidency of the church at the age of 84. On November 2 2006, Hinckley surpassed David O. McKay to become the oldest president in Church history.
Hinckley was known for his acceleration of the building of temples. Before he became president in 1995 there were 47 operating temples in the Church; at the time of his passing, there were 124 – over two-thirds of which had been dedicated or rededicated by Hinckley–and 14 announced or under construction. Hinckley oversaw other significant building projects, including the construction of the Conference Center and extensive renovations of the Salt Lake Tabernacle.
On September 23 1995, Hinckley released The Family: A Proclamation to the World, a statement of belief and counsel regarding the sanctity of the family and marriage prepared by the First Presidency and Quorum of the Twelve. In February 1996, Church membership in countries other than the United States surpassed that of the U.S. membership. 
In November 2000, President Hinckley spoke to the youth of the church and gave them six traits to work on, his famous Six Be's (Be Grateful, Be Smart, Be Clean, Be True, Be Humble, Be Prayerful), which were first introduced in his New York Times Bestseller Stand for Something and later expanded on in Way to Be.
On March 31 2001, he announced the Perpetual Education Fund, a large endowment that provides loans to students in developing nations. On October 22 2002, Hinckley participated in the dedication of the Gordon B. Hinckley Building at Brigham Young University–Idaho in Rexburg, Idaho. This was the first building at BYU–Idaho to be named for a then-living Church President.
In April 2003, Hinckley gave a speech in which he addressed the ongoing war in Iraq. He said, “…as citizens we are all under the direction of our respective national leaders. They have access to greater political and military intelligence than do the people generally,” adding, “Furthermore, we are a freedom-loving people, committed to the defense of liberty wherever it is in jeopardy.” He also noted that “It may even be that [the Lord] will hold us responsible if we try to impede or hedge up the way of those who are involved in a contest with forces of evil and repression.”
In March 2005, Hinckley, together with Thomas S. Monson and James E. Faust, celebrated their tenth anniversary as the First Presidency—the first time in the history of the church that a First Presidency had continued for such a period of time without personnel changes.
On January 24 2006, Hinckley underwent surgery to remove cancerous growths from his large intestine.
In June 2006, Hinckley traveled to Iowa City, Iowa to speak at a commemoration of the 150th anniversary of the start of the Mormon handcart companies. On June 23, 2006—his 96th birthday—Hinckley participated in a groundbreaking ceremony at Brigham Young University in Provo, Utah for a new building that was to be named in his honor. The building was named the "Gordon B. Hinckley Alumni and Visitors Center" and was completed and dedicated on Hinckley's 97th birthday.
On March 31 2007, Hinckley rededicated the Salt Lake Tabernacle after extensive renovation. Hinckley's last public appearance was on January 4 2008, when he offered the prayer at the rededication of the Utah State Capitol.
During his tenure as president, Hinckley gave over 2000 speeches, and traveled half-million miles over a lifetime, as he met with church members and dedicated chapels and temples.
On June 23 2004 (Hinckley's 94th birthday), U.S. President George W. Bush awarded Hinckley the Presidential Medal of Freedom in a ceremony at the White House. The press release put forth by the White House stated:
Hinckley received many educational honors, including the Distinguished Citizen Award from Southern Utah University, Distinguished Alumni Award from the University of Utah, and honorary doctorates from Westminster College, Utah State University, University of Utah, Brigham Young University, and Southern Utah University. He received the Silver Buffalo Award of the Boy Scouts of America, and was honored by the National Conference for Community and Justice for his contributions to tolerance and understanding in the world.
Members of the Westboro Baptist Church (WBC) demonstrated near his funeral, accusing him of having an "ambiguous voice" about the gay lifestyle rather than taking a firm stand against it. One woman explained it was because he "preached that God loves all his children, including the gay ones.