Officials say shots were fired in the mezzanine of the Burke Avenue station at around 10:30 p.m.
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One of the 17-year-olds was shot in the head, arm, and shoulder and did not survive. The other was shot in the hip and is now in serious, but stable condition, authorities said.
Officials say the suspect fled the scene, but investigators have been reviewing surveillance footage from nearby stores.
Sources say whatever led to the shooting started as a dispute between about five teens on the train before spilling out onto the platform.
The Bronx borough president said she had reason to believe the violence is connected to ongoing crew battles in that area.
"We know this is probably a neighborhood issue," Bronx Borough President Vanessa Gibson said. "I guarantee when we do the investigation and we get all of the individuals involved and we identify where they live, I assure you they probably live in the same neighborhood, probably the same development."
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This is the third murder on a train or at a station in New York City so far this year.
Last year's total, 11 homicides, was the highest number the city has seen in the last several years.
"It is only April, it is only April, I worry about my children over the next several months as they are out for the summer season, we cannot accept this violence," Gibson said.
Crime on the subways is down in the last few months and the MTA says the increased police presence that began last year is preventing violence, noting some recent arrests in the subway system.
"Four individuals who were violating quality of life issues, all four may have jumped turnstiles, or gone through a gate were given a civil summons, a scuffle turned up," said NYC Transit President Richard Davey. "They were resisting. It turns out they were carrying weapons on them. The police made an arrest."
The NYPD also announced an arrest in one of the other two subway homicides this year. Isaiah Collazo, 18, of Staten Island is charged with manslaughter in a deadly stabbing last Thursday at the Atlantic Avenue station in Brooklyn.
But people heading to work Tuesday morning were left uneasy after learning someone was killed there.
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"To know that we gotta go back and forth to work and to know that we are not even safe around here because we don't know when we may be bypassing and something like this happens," neighbor Juanita Bailey said.
There is no word on what the fight was about, but sources say the surviving teen who was shot claims he did not know the other victim.
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