The firm were excluded from the bidding process earlier this year.
Stagecoach is starting legal action against the government over its disqualification from bidding for the East Midlands rail franchise - which it currently runs.
Last month ministers also banned it from bidding for two other routes in a row over pensions.
The company says it regrets taking the action - but insists "many fundamental questions remain unanswered."
Meanwhile, the department for transport say they have "total confidence" in their franchise competition process.