On March 15, 2016, the North Dakota State Board of Higher Education announced that Kennedy had been selected as the twelfth President of the University of North Dakota. Kennedy, who had filed his application on January 2, 2016, was in February the third of six finalists to visit the school. He succeeded president Robert Kelley, who retired in January 2016, and Ed Schafer, who served as interim President until Kennedy took office on July 1. He was inaugurated on October 10, 2016.