The 1889 Jefferson Center for Population Health was founded through a collaborative effort. 1889 Foundation, originally known as the Conemaugh Health Foundation, was the philanthropic arm of the Conemaugh Health System.  In September 2014, Conemaugh Health System was sold to Duke LifePoint Healthcare and became a for-profit entity. The Conemaugh Health Foundation was the recipient of funds from that sale and reorganized itself as 1889 Foundation, Inc. in 2015.

Along with the new name came a new mission: 1889 Foundation supports innovative programs and initiatives that improve and transform the overall health and wellness of our region. With that mission firmly in mind, the board of 1889 Foundation soon embarked on a partnership with the Jefferson College of Population Health of the Thomas Jefferson University in Philadelphia to create the 1889 Jefferson Center for Population Health.

On February 26, 2016, a press conference was held to announce the establishment of the 1889 Jefferson Center for Population Health in Johnstown, made possible by a $7.5 million gift from 1889 Foundation. The Center opened in February 2017, and held an open house in March to introduce its inaugural executive director, Dr. Trina Thompson.