[8] Pope Pius IX named Bishop Joseph Sadoc Alemany of Monterey as the first archbishop of San Francisco.

[9] Alemany founded Saint Mary's College in Moraga in 1863, then turned its operation over to the De La Salle Christian Brothers in 1868.

In 1883, Bishop Patrick Riordan from the Diocese of Chicago was appointed as coadjutor archbishop by Pope Leo XIII to assist Alemany.

In 1884, Riordan's first full year in San Francisco, the archdiocese contained 175 priests, 128 churches, and 25 chapels and stations to serve a Catholic population of 200,000.

[15] In early 1894, Riordan protested against the use of Outlines of Mediæval and Modern History by Philip van Ness Myers in San Francisco's public schools.

"[17] In April 1894, the San Francisco Board of Education ruled that the book would still be used but allowed teachers to omit any passages that might "appear in any way to favor or to reflect on the particular doctrines or tenets of any religious sect.

[19] Riordan celebrated open-air Masses for his displaced parishioners, who were living amidst the ruins in temporary shelters, and assured them, "We shall rebuild.

[25] In 1932, Pope Pius XI appointed Bishop John Mitty of the Diocese of Salt Lake as coadjutor archbishop to assist Hanna.

[27] During the 1934 West Coast waterfront strike, President Franklin Roosevelt named Hanna the chairman of the National Longshoremen's Board.

Mitty's first act as archbishop was to direct his installation gift from the clergy to restoring Saint Patrick Seminary in Menlo Park.

In 1968, McGucken became embroiled in a controversy with Reverend Eugene Boyle, a progressive diocesan priest with ties to the Black Panther Party.

Facing intense accusations of racial bias from parts of the public, McGucken asked the San Francisco priest's senate to review his decision.

When Pope John Paul II visited San Francisco in 1987, Quinn arranged for him to meet with several HIV/AIDS patients, including a young boy.

In 2004, O'Shea pleaded guilty and was sentenced to time served in prison for molestation charges and ordered to pay $187,000 back to the archdiocese.

[42] To replace Levada in San Francisco, the pope named Bishop George Niederauer of Salt Lake City.

[43] In 2012, Benedict XVI appointed Bishop Salvatore J. Cordileone from the Diocese of Oakland as the next archbishop of San Francisco, replacing the retired Niederauer.

[44][45] In February 2015, Cordileone told teachers in the archdiocesan school system that they were expected to conduct their public lives in a way that does not undermine or deny the church's doctrine.

[46] Ting and Mulin called for an investigation of working conditions at archdiocesan high schools over the archbishop's proposed morality clauses for teachers.

[48] In April 2015, more than 100 Catholic donors and church members from the Bay Area signed a full-page advertisement in the San Francisco Chronicle appealing to Pope Francis to replace Cordileone.

In April 2022, Cordileone warned Nancy Pelosi, the Speaker of the U.S. House of Representatives and a San Francisco resident, that he would prohibit her from receiving Holy Communion unless she repudiated her promotion of abortion rights.

[55][56] In a 2006 court deposition, it was revealed that in 1992 Bishop Levada had removed Reverend Joseph Baccellieri from ministry after hearing allegations that he had sexually molested three boys during the 1970s.

[citation needed] In 2019, the archdiocese provided documents to California State Attorney Xavier Becerra in preparation for lawsuits after the statute of limitations was temporarily removed in 2020.

[citation needed] In August 2023, the archdiocese filed a petition under Chapter 11, Title 11, United States Code in the San Francisco County Superior Court after it officially confirmed it was declared broke, and could no longer afford any cash to pay off the estimated 500 sex abuse lawsuits.

[62] The archdiocese has the following historic churches: All full-time faculty, librarians, and counselors at Archbishop Riordan, Junipero Serra, Marin Catholic, and Sacred Heart Cathedral high schools are represented by The San Francisco Archdiocesan Federation of Teachers, Local 2240, a labor union affiliate of the California Federation of Teachers (AFT, AFL–CIO) under a collective bargaining agreement.