It is situated between the Columbia City and Beacon Hill stations on the 1 Line, which runs from Seattle–Tacoma International Airport to Downtown Seattle, the University of Washington, and Northgate as part of the Link light rail system.

[4] Part of the $10–20 million plan would move bus stops at the existing off-street transit center to the plaza under Mount Baker station, with bus lanes and a special bus-only street on South Winthrop Street between Rainier Avenue and Martin Luther King Jr. Way; the proposal was funded as part of the "Move Seattle" levy passed by voters in November 2015.

[13] The west side of Mount Baker Station is occupied by the former University of Washington Consolidated Laundry and is proposed for redevelopment into a mixed-use affordable housing complex along with an adjoining property owned by Sound Transit.

[15][16] A failed rapid transit proposal published in 1928 by the Seattle Traffic Research Commission recommended that a future southern extension on Rainier Avenue terminate at either McClellan or Winthrop streets in Mount Baker.

[17] A modern light rail system for Seattle was proposed in 1995, including a station at the intersection of Rainier Avenue and McClellan Street in Mount Baker.

[25] Sound Transit awarded the construction contract for Mount Baker station and the Beacon Hill tunnel to Japanese firm Obayashi in June 2004 for $280 million, the costliest component of the Central Link project.

The 30,000-square-foot (2,800 m2), brick-clad station building contains the 400-foot-long (120 m) side platforms situated 35 feet (11 m) above a plaza with ticket vending machines at ground level.

[37] Sheila Klein's "Sky Within" consists of six chandeliers, recycled from former street lights, that are suspended above the plaza level on the underside of the train guideway.

[41][42] Mount Baker station is part of Sound Transit's 1 Line, which runs from between Lynnwood, the University of Washington campus, Downtown Seattle, the Rainier Valley, and Seattle–Tacoma International Airport.

[45][46][47] On weekends, a Trailhead Direct shuttle connects Mount Baker Transit Center to several popular hiking trails in the Issaquah Alps.