[4] In 2001, MBTA Framingham/Worcester Line and Amtrak operations were shifted to a new set of platforms nearby, which have high-level sections for handicapped-accessible boarding and a footbridge for crossing the tracks.

[6] After being replaced, it was moved slightly west and converted to a freight house – a function it served until it was demolished in the 1960s.

This line, later called the Agricultural Branch Railroad, was realigned near Framingham Center and extended to Pratts Junction in Sterling in 1855.

[5] Framingham began to be used occasionally as a short turn terminus for Boston-bound commuter trains in the early 1860s and continuously as such after 1864.

[9] Beginning in 1881, the Boston & Albany began a massive improvement program that included the building of over 30 new stations along its main line as well as the Highland branch, which it bought in 1883.

Famed architect H. H. Richardson was hired to design nine of these stations, including South Framingham which was commissioned in October 1883.

[6] The station is a prime example of the Richardsonian Romanesque style, built of rough-hewn granite with contrasting details.

The dominant roofline, dormers, arched bow window, and wooden interior are typical of the style.

[10] A small square baggage room was built in the same style just east of the station, near the Concord Street (Route 126) grade crossing.

After the Boston & Albany was acquired by the New York Central Railroad in 1900, third and fourth tracks were extended in 1907 to South Framingham from Lake Crossing station in Wellesley.

In 1919, Agricultural branch trains were cut to Framingham, requiring a transfer to continue Boston or Mansfield.

[12][8] The modern Amtrak Lake Shore Limited was established 4 days later, and has provided intercity service via Framingham ever since.

[6] On January 17, 1975, the building was added to the National Register of Historic Places as Framingham Railroad Station.

A footbridge with two elevators was built to allow passengers to reach the outbound platform without crossing the tracks, which carry slow-moving CSX freight service as well as MBTA and Amtrak trains.

[9] Average weekday ridership is 1,130 passengers, making Framingham the second-busiest station on the line outside Boston (after Worcester).

[3] Framingham also has Amtrak intercity service via the daily Lake Shore Limited, which runs to Chicago's Union Station via Albany–Rensselaer.

In October 2016, the MetroWest Regional Transit Authority (MWRTA) took over management of the station from the MBTA under a lease agreement.

[18] An additional parking lot was opened inside the wye on the north side of the station in August 2017.

Unlike most other mid-sized cities in Massachusetts, Framingham still has significant level crossings in the downtown area.

The frequent blockage of the crossing by passing trains reduces capacity in the intersection by 21% during the morning rush and 16% in the afternoon, resulting in delays and traffic jams in the downtown area.

[32] The most recent, a 2009 study of the downtown area, examined the possibility of depressing Route 126 under the grade crossing and intersection as well as several other alternatives including bypasses.

South of the station platforms, the remaining rarely-used stub of the Milford Branch crosses Waverly Street (Route 135) at grade.