The accessible terminal station has a single island platform serving the two tracks of the Union Square Branch, which parallels the Fitchburg Line.

Several station sites and alignments were considered, with the Prospect Street location and the route along the Fitchburg Line chosen in 2009.

[3]: 12.1-5  A starter booth is located at the east end of the platform, with an at-grade emergency exit walkway leading to Allen Street.

[1]: 9 The station entrance plaza is located on the east side of the Prospect Street bridge, next to a small utility building.

[9][10][11] Like Somerville station and other local stops, Prospect Street was primarily served by Lexington Branch trains in the mid-19th century.

[9][14][15] Planning to eliminate the eleven remaining grade crossings in Somerville, five of which were on the Fitchburg Route mainline, began in 1900.

[16] In 1906, the city engineer proposed to raise 1.8 miles (2.9 km) of the line between Beacon Street and Somerville Avenue to eliminate the five level crossings, but that scheme was not adopted.

[17] After the Somerville Avenue grade crossing was eliminated in 1908–09, work began in April 1911 to raise Webster Street above the tracks.

[27][28] Adding an MBTA Commuter Rail Fitchburg Line station at Union Square has been considered; by 2003, a stop was expected to open within five years.

[31] Various 20th-century proposals called for rapid transit along the B&M Southern Division (now the Lowell Line) to West Medford or beyond; the nearest station to Union Square was to be about 0.4 miles (0.6 km) to the east.

The analysis studied a variety of light rail and bus rapid transit extensions, including a branch to Union Square.

[46] The DEIR, released in October 2009, selected the Fitchburg Line routing on the basis of lower cost, higher reliability due to grade separation, and less property acquisition required than the other alternatives.

This would have allowed the lower entrance to be closed to accommodate the outbound track, were a proposed further extension to Porter to be built.

[50][51] A further update in June 2013 removed a mechanical penthouse, modified the lobby designs, and added bicycle racks near the upper entrance.

Through the Somerville Redevelopment Authority, the City would acquire $8 million worth of land for the station and grant the MBTA a permanent easement, while retaining the rights for transit-oriented development overhead.

In return, the MBTA and MassDOT would pay for cleanup costs at the site, begin construction by the spring of 2014, and open the station no later than "late 2016-early 2017".

[63] At that time, cancellation of the project was considered possible, as were elimination of the Union Square Branch and other cost reduction measures.

The new design for Union Square removed the direct access from the Prospect Street overpass, with entrance to be only from the plaza on the north side of the station.

E. Denise Simmons criticized the scaled-down station designs at Union Square and East Somerville for having long ramps rather than elevators, saying they were not sufficient for accessibility.

As with the GLX as a whole, the Union Square redevelopment has been criticized by local advocates for its potential to cause gentrification and community displacement.

[75][76] A 2014 study found that the areas around Union Square and East Somerville stations were expected to have the highest rent increases – up to 67% in some instances.

[75] The USQ mixed-use development in Union Square, which is primarily replacing light industrial buildings, is intended as an anti-gentrification measure by increasing housing supply and subsidizing nearby households and businesses at risk of displacement.

[78] In November 2019, the USQ developer, US2, agreed to fund an elevator connecting the station to the Prospect Street bridge.

[88] Electrical work began in mid-2021; canopy lighting was functional and next-train countdown signs were in place by that November.

[105] The Union Square Branch was closed from September 18 to October 10, 2023, during repairs to Squires Bridge, which carries the McGrath Highway over the tracks.

In February 2022, the Cambridge City Council signed a resolution requesting work around Union Square station not to interfere with such an extension.