The company accuses the city's firefighters of "failing to exercise ordinary care," according to the lawsuit.
The incident took place on March 1, 2009 near the Lonyo and John Kronk intersection. The train's engineer spotted Ladder 13 on the tracks and applied the emergency brakes, but was unable to avoid the crash.
Amtrak says it has suffered more than $75,000 in losses.
Former Executive Fire Commissioner James Mack -- who was removed from the post in January -- was very critical of the engine's crews following the wreck.
"I'm very upset," he told the newspaper. "I'm going to make it known that this is not acceptable and we'll do some training."
Crews had responded to an earlier collision involving a car and a tractor trailer on the city's southwest side.
As the train approached, four firefighters jumped in the ladder truck and tried to move it in time, but it was too late. They were T-boned by the train and dragged before coming to a rest on the tracks.
One firefighter was injured in the crash and was treated for a gash to his head. No other firefighters were seriously injured.
One passenger aboard the trained complained of pain about an hour following the crash.
The $600,000 ladder truck was totaled in the wreck.
