The structure burned in 1893 and was rebuilt as a Victorian eclectic depot with Richardsonian influences—one of the few such buildings in the state constructed from wood rather than stone.

After a fatal collision on February 16, 1881, the state Board of Railroad Commissioners recommended the junction be grade-separated.

[10] The station was designed by the chief engineer of the NY&NE and constructed for a cost of $10,000 (equivalent to $277,886 in 2023).

[6] A separate structure to the south was built to house the signal functions; the tower on the new station was lower and smaller because it was no longer needed to control the interlocking.

[2] The newly formed Massachusetts Bay Transportation Authority began subsidizing suburban commuter rail service on the Franklin Branch on April 24, 1966.

[14] Penn Central, which had absorbed the bankrupt New Haven Railroad, added an antenna tower at the station on November 14, 1971.

[6] On January 27, 1973, the MBTA purchased most of the Penn Central commuter lines, including the Franklin Branch and Walpole station.

[2][15][6] Concrete platforms and a new parking lot south of the station building were built in July and August 1978.

[6][13] On June 3, 2004, the MBTA board approved a $1.4 million plan for adding 200 parking spaces to the station.

[19][6] A coffee shop operated inside the north wing of the station building until 2009; it was replaced by a similar business several years later.

[19] The MBTA performed roof repairs in 2012–13; original slate tiles were replaced by modern PVC, and some finials and cresting were removed.

[26][27][28] The service switches from the Franklin Branch to the Framingham Secondary at Walpole using Lewis's Wye, but does not serve the station.

[29] The MBTA completed a study in 2010 to determine the feasibility of extending full-time commuter rail service to Foxboro.

[6][29] A year-long pilot of full-time Foxboro service (mostly using extended Fairmount Line trains) began on October 21, 2019.

[30][14] The pilot was put on hold in November 2020; limited midday Foxboro service resumed on May 23, 2022.

[31][32][33] A new one-year Foxboro pilot began on September 12, 2022; the service was made permanent effective October 2, 2023.

These platforms do not require alterations to the existing platforms, thus skirting federal rules requiring full accessibility renovations when stations are modified, and were intended to provide interim accessibility at lower cost pending full reconstruction.

A further phase is planned to add double track through Walpole station and northeast to Norwood Central.