The 64-year-old was hit by an out-of-service northbound F train near the Hoyt -Schermerhorn Streets station just after midnight.
The train conductor immediately pulled the emergency brake and the rest of the team killed the power.
Police and EMS responded quickly and took him to the hospital with head trauma.
"The employee is responsive. He opens his eyes, but that's probably the extent of his communication at this point," Senior Vice President of New York City Transit Department of Subways Demetrius Crichlow said.
The man was working as a flagger in a crew of four inspecting rails overnight. A flagger alerts oncoming trains that there are crews up ahead.
The MTA is investigating exactly what went wrong.
This incident comes after MTA employee Hilarion Joseph, who was also working as a flagger, was hit and killed by a train in Manhattan.
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