Wedgemere and Winchester Center are "Zone 1" stops on the MBTA Commuter Rail Lowell Line. The stations are conveniently located within walking distance of one another. The Lowell Line goes from Lowell to Boston's North Station, where one may connect with the "T", Boston's subway system. The nearby Anderson Regional Transportation Center, located off I-93 (Commerce Way exit), serves as a station for Amtrak's Downeaster train, which travels through New Hampshire and ends in Brunswick, Maine. While passing through Winchester, this train does not stop at either of the town's two train stations.

There are bus routes that go through Winchester to surrounding towns including Medford, Arlington, and Cambridge. The Massachusetts Bay Transportation Authority's (MBTA) Orange Line bus route No. 134 travels between North Woburn and Wellington Station in Medford. The MBTA Red Line bus service No. 350 connects the Burlington Mall to the Alewife station in Cambridge.

During rush hour, a commuter express bus travels from Cummings Park in Woburn to Boston. Anderson Regional Transportation Center also features a Logan Express shuttle bus service that runs every 30 minutes to Boston's Logan Airport, as well as a paid shuttle service to Manchester New Hampshire Airport (reservations required in advance)