The incident happened at the 46th Street station in Astoria around 3:30 a.m.
The 58-year-old victim identified as Louis Moore was removed from the tracks just after 5 a.m., and other transit employees were visibly upset by what they had seen.
At this point, it is unknown why the man was on the tracks. It is unclear if there was scheduled track work or some other issue.
The signal maintainer is the first transit worker to be fatally struck by a train since 2007, when a veteran trackman was crushed by a G train at the Hoyt-Schermerhorn station in Brooklyn. Another worker died in 2010, when he slipped and fell onto the third rail of elevated tracks in Queens.
It has been the second-longest stretch without a employee death by train since 1946. Nearly 240 transit workers have been killed on the job since 1946.
This time, the worker reportedly fell off a ladder while climbing up to the platform and was was struck by a Jamaica-bound E train. He was pronounced dead at the scene.
Jermaine Ramos was a passenger on the train at the time.
"We felt this thump, so we knew somebody was probably on the tracks," he said. "So they stopped the train, and the had cops told us to get out. They didn't tell us anything like what happened, they just wanted to move everybody as quickly as possible."