Wilson became a through station in 1908 when the Northwestern Elevated Railroad was extended to Central in Evanston (using tracks belonging to the Chicago, Milwaukee and St. Paul Railway).

The extended right-of-way allowed for a retail structure partially beneath the elevated tracks, which was designed by Frank Lloyd Wright in 1909, known as the Stohr Arcade Building.

An elevated stub line from the station is a remnant of a connection into the former Buena Interchange Yard, where freight was exchanged with the Chicago, Milwaukee and St. Paul Railway.

The CTA stopped carrying freight in the early 1970s and the stub was demolished south of Montrose Avenue.

In 2010, further demolition split the remaining stub into two sections to allow for new Truman College construction.

[6] The rebuilt station has a new main station entrance on the south side of Wilson, elevators, escalators, wider stairwells, additional turnstiles, new lights, new signage, additional bike parking, new security cameras, new train trackers, two island platforms to provide cross platform transfers between the two lines, and two auxiliary entrances: one at Sunnyside Avenue and one on the north side of Wilson.

Northbound Red Line trains will stop on the eastern half of the southbound platform until the end of the project.

The east platform and the auxiliary entrance on the north side of Wilson opened for service on October 23, 2017.