The station has a single side platform serving the southern track of the two-track Northeast Corridor.

[6] A small wooden westbound shelter, similar to other Shore Line stops east of New Haven, was added in the 1950s.

[9][10][11] The Clamdigger was reinstated on January 8, 1978, with commuter-based flag stops added at Groton, Clinton, Madison, Stony Creek, and Branford.

[17][6] The Madison Senior Center, which had been a possible reuse of the station, was rebuilt on Old Route 79 as an exact replica; it was demolished around 2011 during the construction of a new ambulance facility on the site.

The modern Madison station opened at the beginning of Shore Line East service on May 29, 1990.

[2] By 2012 it was to go out to bid in 2013, but this was indefinitely delayed as platform construction at busier Branford and Guilford and electrification work for future M8 service were prioritized instead.