The station first signed on the air on May 3, 1979 as a satellite of KLRN in San Antonio. Before KLRU's sign-on, KLRN had served both cities from the Jesse H. Jones Communications Center on the campus of the University of Texas at Austin. Channel 18 had been allocated to Austin as a noncommercial frequency in the early 1950s, but it was thought that a UHF station would not be nearly be adequate enough to provide educational television for a market that stretched from Mason in the west to La Grange in the east. This left Austin as one of the largest cities without its own PBS station.

From the day KLRU signed on, however, KLRN's owner, the Southwest Texas Public Broadcasting Council, set about making it a separate station focused on Austin. Only a year after KLRU hit the airwaves, it received its own Austin-based governing board, though it continued under the ownership of the Southwest Texas Public Broadcasting Council. In 1984, after KLRN moved to a new tower in San Antonio, KLRU adopted a separate programming schedule. In 1987, the two stations finally went their separate ways, with KLRU coming under the ownership of the Capital of Texas Public Broadcasting Council, which continues to own the station today.