Officers were called after someone heard the cat crying for help at 32nd Avenue and 99th Street at 8:30 a.m.
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The kitten was apparently swept into the sewer during the overnight storms.
ESU Det. Brian Hirsch, a 20-year veteran, climbed eight feet down into the filthy sewer water and spent 45 minutes trying to coax the kitten to come closer so he could grab it.
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The cat's owner was there to quickly claim the pet who was frightened, but not hurt.
The NYPD added that Det. Hirsch was "feline good" after the rescue.