Operated by the Capital District Transportation Authority (CDTA), the current station seen was completed in September 2002 and opened on September 22, 2002. It was designed by the Schenectady architecture firm Stracher–Roth Gilmore and the New York firm Vollmer Associates, with Ryan-Biggs of Troy providing structural engineering, Sage/Engineering Associates providing MEP engineering services, Erdman Anthony of Troy providing facilities engineering, and constructed by U. W. Marx/Bovis joint venture.
The intermodal station replaced two previous terminal buildings, one built in 1968 and the other in 1980. The 1968 building, which is riddled with asbestos, has since been torn down to make more room for the station's parking facility, just before the entrance to the parking garage. Before 1968, trains stopped at Union Station in Albany itself. That building, located on Broadway, now houses the northeast headquarters of Bank of America. The New York Central Railroad had plans to leave Albany, in part because Interstate 787 needed the space occupied by a rail yard, but the move took place under Penn Central's watch.