Prebys gave his all-time largest gift of $100 million to the Sanford-Burnham Medical Research Institute in June 2015, to support its 10-year strategic vision to develop and implement innovative medical treatments that can have lasting, positive effects on the field of healthcare. The gift resulted in the renaming of the institute, which is now known as the Sanford Burnham Prebys Medical Discovery Institute. In October 2015, Prebys donated $20 million to the Indiana University Kelley School of Business to fund the construction of a new campus amphitheater and the Kelley School of Business Conrad Prebys Career Services Center, which began construction in summer 2015. He visited the campus shortly after the gift was made public, where he was greeted with a warm welcome by students, faculty, and Kelley School of Business dean Idie Kesner. Many of the school's students created posters and cards to thank Prebys for his generosity and philanthropic vision for the forthcoming career services center that will bear his name.
In June 2015 Prebys was awarded an honorary Doctor of Humane Letters from San Diego State University's College of Business Administration.