The station signed on in 1979 as WJHU, a 10-watt student-run station owned by Johns Hopkins University. It took over from a carrier current station that had operated under the same calls on AM 830 since 1945. Originally a typical freeform college radio station, it boosted its power to 25,000 watts in 1985, allowing it at least secondary coverage of the entire Baltimore/Washington corridor. Soon after the power increase, Johns Hopkins converted the station into a full-time professional operation, allowing it to become Baltimore's NPR member station. It originally aired a mix of classical music and NPR programming, but on June 23, 1995, switched to a primarily news/talk format.
Johns Hopkins put the station up for sale in 2000 due to the expense of maintaining it, as well as a change in focus that no longer included radio. In 2002, Your Public Radio Corp., a community group, bought the station and changed its calls to WYPR. In 2004 Your Public Radio Corp. bought religious broadcaster WJTM in Frederick, which became a relay of WYPR with the call letters of WYPF. WYPF's signal also covers Hagerstown. On July 30, 2007, Your Public Radio Corp. bought Ocean City, Maryland alternative rock station 106.9 WRXS, which began simulcasting WYPR starting September 10, 2007. That station was renamed WYPO on October 3, 2007. The three stations provide at least grade B coverage to almost two-thirds of Maryland.
For much of the time from the late 1990s to 2008, it operated at only 10,000 watts. While this provided a decent signal to Baltimore itself and most of its close-in suburbs, many of Baltimore's outer suburbs, including Annapolis, only got a grade B signal. In 2008, it increased its power to 15,500 watts, giving it a coverage area roughly comparable to the other major Baltimore stations. However, since its transmitter is located in northwestern Baltimore, some areas of Harford County get only a grade B signal. Furthermore, its signal is not as strong in the southern part of the metro area because it must conform its signal to protect Washington's WAMU, at nearby 88.5. While the University of Maryland student station, WMUC, broadcasts on the same frequency as WYPR, WMUC is designated as a class D station and thus its signal is not protected, rendering both stations practically unlistenable in parts of Prince George's County, Montgomery County and Northeastern DC due to WYPR's interference with WMUC.