[3][5] The station is primarily wood on a brown brick base, with Georgian Revival architectural elements such as Palladian windows on the east and west facades.

It is clad in wood shingles, which had become popular in New England in the late 19th century as a result of interest in colonial history.

The station was in poor shape and closed to passengers; although ownership was uncertain, the property was claimed by Amtrak.

[3] The rails were moved slightly away from the station building in 1981 when the Mystic River bridge to the west was rebuilt on a new alignment.

[3] In 2001, the Greater Mystic Chamber of Commerce began operating a tourist center in the station.

After the Chamber's lease expired, the station building was closed on March 15, 2015, though Amtrak service continued.

[9] Three proposals were submitted for reuse; a Rhode Island–based company won the lease in June 2015 to use the building as a cafe and gift shop.

[11] The shop, Mystic Depot Roasters, has seating and a ticket machine for Amtrak passengers; it opened on September 30, 2016.