In early 2020, Pioneer Square station served as a transfer point between trains with a temporary center platform as part of construction for the 2 Line.

[11] In 1911, civil engineer Virgil Bogue presented a comprehensive plan for the city of Seattle, including a rapid transit system centered around a "trunk" subway under 3rd Avenue, passing through Pioneer Square and the growing commercial and retail district to the north.

[19][20] The failure of the Forward Thrust ballot measures led to the creation of Metro Transit in 1972, operating bus service across King County.

[21] Metro Transit began planning a bus tunnel through downtown Seattle in the 1970s, to be eventually converted to use by light rail trains.

[25][26] Metro awarded a $44.1 million contract to a joint venture of Atkinson and Dillingham companies to build the tunnel's 3rd Avenue segment as well as Pioneer Square station.

[29] Work in the tunnel station was also blamed for shaking in the City Hall and Public Safety Building, requiring monitoring equipment to be set up by Metro.

In late 1987, Atkinson-Dillingham was forced to remove steel beams used for temporary shoring at the station box after unknowingly sourcing it from South Africa.

[33][34] Tunnel construction was completed in June 1990, and was celebrated with a soft opening of Pioneer Square station and the re-opening of Prefontaine Park.

[35] During preparation for the resurfacing of 3rd Avenue above the new tunnel station, workers discovered an 11-foot (3.4 m) cable car flywheel that had been buried after service on the Yesler Way line ceased in 1940.

[45] Ownership of the tunnel, including its stations, was transferred to Sound Transit in 2000 but returned two years later to King County Metro under a joint-operations agreement.

The renovation included the installation of new rails, a lowered roadbed at stations for level boarding, new signalling systems and emergency ventilation.

[55][56] As part of East Link Extension construction for the 2 Line in early 2020, Pioneer Square station was outfitted with a temporary third platform in the center to allow passengers on terminating single-tracked trains to transfer.

[61] Pioneer Square station consists of two underground side platforms used to load passengers onto trains and buses, a mezzanine level, and several surface entrances.

[62] The station has two mezzanines on its north and south ends, with the center portion opened to the platform below; all levels are connected by a series of eight escalators, six elevators, and stairs.

The south mezzanine has a single entrance to Prefontaine Park at Yesler Way between 2nd and 3rd avenues, under a large pergola similar to an older streetcar shelter in Pioneer Square.

The Prefontaine Park entrance houses an 8-by-50-foot (2.4 by 15.2 m) ceramic mural created by artist Laura Sindell, depicting people-like figures, a 19th-century quilt pattern, a Coast Salish basket design, and a dugout canoe.

[62][68] The platform level also makes extensive use of red and gray granite, matching the King County Courthouse and former Public Safety Building,[65] and railings that resemble hitching posts and hanging lamps.

It was created in 2009 by Christian French as part of the Stellar Connections series and its points represent nearby destinations, including Seattle City Hall, Colman Dock, the Klondike Gold Rush National Historical Park, and King Street Station.