The station signed on in 1949 as WHKW, originally licensed in Chilton. It was the third FM station in the Wisconsin Educational Radio Network, forerunner of Wisconsin Public Radio. In 1973, WHKW moved to the WPNE-TV transmitter site in Green Bay after that station's launch the year before, and became WPNE-FM;[2] it also supplanted an additional Wisconsin Educational Radio Network transmitter, WHMD-FM 91.5 at Suring, which had signed on in 1965.[3]
Unusual for a market of its size, as of the end of 2022, WPNE is the only radio station in Green Bay, the Fox Cities, and the Lake Winnebago cities which transmits an HD Radio broadcast; WPNE-HD2 transmits WPR's HD Classical Network full-time.