The station operates on two different schedules: The regular schedule, which runs during the school year, operates from 9 A.M. until 2 A.M. During school breaks, including the summer, the station operates from noon until 2 A.M. When the station is not programming live from its studios, the station rebroadcasts WVIA-FM programs, including some National Public Radio, or uses the automation system. Included with WVIA’s classical format are a variety of popular shows, such as Morning Edition, A Prairie Home Companion and Car Talk.
Programming Mondays-Fridays consist of the station's format of modern and alternative rock. Throughout the week there are specialty shows of many other genres including classic rock. Saturday programming consists of country and bluegrass. Sundays have a variety of specialty programming including blues, techno, Susquehanna University's church service, classical, and the Grateful Dead. WQSU also airs a wide variety of news and sports coverage.