One commuter captured an image of the vandalism at the northbound 20th Avenue station before workers applied a fresh coat of paint to the area to remove the symbol.
The MTA issued a statement saying in part, there is "no place for this sort of signage and language in our system."
Officials said law enforcement has been notified.
The incident comes as elected officials call attention to an increase in the number of anti-Semitic crimes in the city and around the country.
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