In the first, a person was struck by a Metro-North train on the Upper East Side early Sunday morning.
The male victim, who is described as a trespasser, was pronounced dead at the scene at about 2 a.m.
He was struck inside a tunnel in the vicinity of East 67th Street.
The accident forced a shutdown of power and an interruption of service for several hours on both northbound and southbound trains.
The MTA says service was restored by 5 a.m.
The other incident took place in Soho, where a man was hit just after 3 a.m.
Investigators say he appeared to be wallking between cars on a northbound Q train when he fell on the tracks near Prince Street.
The man was discovered by the train's operator, who had gotten out to find out what was keeping the train from moving.
Service on Q and N trains was interrupted while police investigated, but later resumed.