It was last served by Amtrak's daily Empire Builder, with service from Chicago, Illinois to Seattle, Washington or Portland, Oregon.

Midway had been a station stop for every Amtrak route in Minnesota until May 2024, when the Borealis began service using Saint Paul Union Depot.

Amtrak had opted to consolidate all of its Twin Cities services in Minneapolis when it began operation in 1971, shuttering the Saint Paul Union Depot.

On May 7, 2014, Amtrak moved its Twin Cities-area stop to the renovated and reopened Saint Paul Union Depot.

[5] After a short time of Midway station being closed to the public, but still serving as a service stop for the Empire Builder, the building was abandoned, ending up on St. Paul's vacant property listings.

[13][9][14] As part of the TCMC project (the Borealis service) the station was noted as being a potential improvement if deemed necessary by Amtrak.

Under the proposal the station would be converted to a layover facility, serving as a crew base, light equipment servicing, cleaning, and kitchen.