During his freshman year Niederauer changed course and decided to enter St. John's Seminary in Camarillo, from where in 1959 he earned a Bachelor of Philosophy degree.

[1] He was appointed the eighth Bishop of Salt Lake City by Pope John Paul II on November 3, 1994.

Niederauer received his episcopal consecration on January 25, 1995, from Cardinal Roger Mahony, with Archbishop William Levada and Bishop Tod David Brown serving as co-consecrators.

As bishop he was seen as "the most approachable of persons and one whose homilies were almost magical in their ability to make potentially difficult Scripture passages and theological concepts comprehensible and applicable – even inspiring – in our daily lives.

"[2] On December 15, 2005, Pope Benedict XVI named him to succeed William Levada as the eighth Metropolitan Archbishop of San Francisco, following Levada's appointment to Pope Benedict's former post of Prefect of the Congregation of the Doctrine of the Faith in the Roman Curia.

[4] On July 27, 2012, the apostolic nuncio to the United States announced that the Holy See had accepted Niederauer's letter of resignation, and Salvatore J. Cordileone was appointed the Archbishop-elect of San Francisco.

Wrote the San Francisco Chronicle, "Niederauer drew in the Church of Jesus Christ of Latter-day Saints and proved to be a critical move in building a multi-religious coalition—the backbone of the fundraising, organizing and voting support for the successful ballot measure.