The Fitchburg Railroad opened through Belmont on December 20, 1843, but no station stop at Waverley Square existed until about 1860.

The tracks originally ran through the square at grade, with level crossings of Trapelo Road and Lexington Street.

In August 1951, the town approved an agreement with the state and the B&M for a $1.125 million state-funded project to lower the tracks 18 feet (5.5 m) to eliminate the crossings.

[5] The work was completed in 1952, at which time Central Mass Branch trains were moved from their parallel tracks onto the Fitchburg main.

[6] Weekend service was discontinued at the two stops on January 30, 1981 as part of general cutbacks, but restored on December 6, 1993.