WYIN evolved from non-commercial station WCAE, originally licensed to the Lake Central School Corporation in St. John and airing on channel 50. The school system was unable to maintain broadcast operations and the station went dark in 1984. The station's license was swapped with Metrowest Corporation's WGMI, a construction permit on channel 56 licensed to Gary that had never been built. Metrowest eventually took the channel 50 signal to air as commercial station WPWR-TV. The non-commercial license (now reassigned to channel 56) was secured by the founding group of WYIN, who took it on the air on November 15, 1987.

For many years, WYIN fought to try to have its transmitter relocated to either the Sears Tower or the John Hancock Center in Chicago's Loop neighborhood. This was opposed by WTTW and WYCC, both of which were very critical of the move as it would make WYIN a full competitor in the Chicago market. Currently, WYIN pays a lower license fee for carriage of PBS programs; by moving the transmitter to Sears Tower or John Hancock, WTTW claimed they would get the same coverage and pay less for their programming, leaving WTTW at a disadvantage as well as taking pledges from the station. WYIN eventually ended all efforts[when?] to try to move its aging broadcast transmitter and instead built a new transmitter tower in Cedar Lake, Indiana.