Authorities say the fire broke out in the house on Van Duzer Street in Grymes Hill just before 10:20 a.m.
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Heavy flames shot out the sides of the two-story duplex as firefighters arrived.
"The entire second floor was engulfed in flames so much that the fire was coming down the stairs. We found the victims inside, all unconscious and needing to be removed," said FDNY Chief of Department John Hodgens said.
Firefighters we're able to set up a hose into the house and quickly put out the flames.
The children were pulled from the home and firefighters began CPR until emergency medical technicians arrived.
A 5-year-old girl died at the scene while a 6-year-old boy was pronounced dead at the hospital, officials said.
Two boys, ages 5 and 10, were critically injured.
Two other children, a 12-year-old girl and 14-year-old boy, were less seriously injured.
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The teen was the oldest person at the home at the time of the fire.
FDNY Commissioner Laura Kavanagh said the children are believed to be siblings and their mother was being treated at the hospital for shock.
One firefighter was treated for minor injuries.
The family that lives on the other side of the duplex was able to make it out safely.
The fire is believed to have started in "the back of the second floor," Kavanagh said.
The cause is still under investigation.
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