The station is located on a viaduct in downtown Winchester, with two accessible side platforms serving the line's two tracks.

The Boston and Lowell Railroad opened between its namesake cities in 1835; local stops were added soon after.

[9] In the early 1950s, the B&M began planning a project to raise the tracks of the New Hampshire Main Line and the southern end of the Woburn Branch for a mile through Winchester, eliminating troublesome grade crossings downtown.

[10] Construction began in 1955; boxy two-story brick stations opened at Wedgemere and Winchester Center in 1957.

[3][11] Until 1981, the Woburn Branch diverged from the main line just north of the Winchester Center platforms.

In September 2008, the MBTA approved $1.4 million in platform and ramps repairs, as well as electrical and lighting work, at the station.

[13] The work was completed in 2010; the MBTA intended to renovate the station before the 5-year life of the platform patches was reached.

A gauntlet track may be installed to allow CSX Transportation freight trains to pass.

[38][39] Work was delayed by plumbing code compliance issues, supply chain issues, and reduced work windows due to a September–November 2023 diversion of Haverhill Line service over the Lowell Line.

[45] However, delays in the completion of the elevator work resulted in the reopening date being pushed back a day to October 1st.

[46] As of December 2024[update], construction is 80% complete; the remaining portion is expected to open in July 2025.

[47] As of 2024[update], transit oriented development with 56 residential units is planned to replace the MBTA-owned and town-owned surface parking lots on the south side of Waterfield Street.