Many trains, including the Stockholm commuter rail (Pendeltåg), also leave the main line to connect Uppsala with Stockholm-Arlanda Airport.

Many local bus routes run through or near the station grounds as well, and there is a large area set aside for bicycle parking.

This project included: a new station building, just to the south of the existing one — constructed 2009–2010; an underpass under the tracks for pedestrians and bicycles; Stadshusgatan, a busway on the west side of the station, so that passengers no longer need to cross Kungsgatan to reach southbound buses (northbound buses remain on the near side of Kungsgatan); Stationsgatan, a new road extending Storgatan on the east side of the station; a new car park, and more bicycle parking; a new public square, and various beautification projects.

[7] On 29 July 2018, the station's pedestrian underpass was flooded due to heavy rain after a long dry period.

Several people decided to use the underpass as a swimming pool, bringing floats, snorkeling gear, and water pistols.

[17][18] Inter-city rail services run west to Falun and Mora, north to Gävle and Ljusdal, and south to Stockholm and Linköping.

[19][20] Regional services run to Stockholm, with an approximate frequency of 2 trains per hour, and occasionally to Örebro as part of the Mälartåg network.

[26] As of 13 December 2020, Vy Tåg operates night trains to Narvik and Luleå after taking over from SJ.