Primary Children's Hospital had its beginnings in the efforts of The Church of Jesus Christ of Latter-day Saints (LDS Church) to provide adequate medical care to citizens of the Western United States. An LDS organization and building, named "Deseret Hospital", was first founded in 1882 in Salt Lake City, but it closed for financial reasons in 1900. In 1905 another effort resulted in the "Dr. W. H. Groves Hospital" in Salt Lake City, funded largely by a bequest from an English dentist who had migrated to Utah. Its successor, LDS Hospital, also in Salt Lake City, continues today.
In 1911, some LDS Church leaders, including May Anderson and Louie B. Felt, pushed for a separate facility geared to needs of infants and young patients. By 1913 a children's ward had been established at LDS Hospital, and by 1922 a separate facility for children was established in a large Salt Lake City house. It was run by the Primary Association (the auxiliary organization of the LDS Church which deals with teaching and care of children), thus the name. During those years, the LDS Church encouraged its members to donate to the hospital's fund by an annual fundraising effort, "Pennies By The Inch", in which members were asked to donate as many pennies as they were tall (in inches).
On February 12, 1952 the hospital moved to a larger building located near the top of the Avenues area of Salt Lake (the hilly portion of northeast Salt Lake City). It was substantially enlarged in 1966, gaining nearly twice its original area.
In 1974 the LDS Church decided to divest itself of the ownership and operation of several of its non-church-related activities such as health-care facilities. In 1975 its hospitals were turned over to the Intermountain Health Care group, which still owns and operates Primary Children's Hospital. However, in 1990 the Avenues facility was closed and was transferred to a larger facility on the University of Utah medical campus. University faculty provide care for patients at Primary Children's Hospital, and the University of Utah pediatric residency program and medical school use Primary Children's Hospital as their pediatric training site.