The incident happened at Congregation Kerem Shlomo on East 27 Street at around 9:30 p.m.
When the victim approached the location, police say he was immediately accosted by a 20-year-old man yelling, "(expletive)Jews! I'm going to (expletive) you up. I see you Jews are racist."
The suspect, Hesham Ghonim, then punched the victim in the face, according to authorities.
Ghonim was later arraigned and is being held on $5,000 cash bail.
Flatbush Shomrim Safety Patrol tweeted out a picture of the suspect during the arrest.
He was charged with assault, assault as a hate crime, aggravated harassment, resisting arrest, criminal mischief and menacing.
The victim was taken to Lutheran Medical Center for treatment.
He sustained a contusion on the face and briefly lost consciousness.
Police say the victim works for Customs and Border Protection and was in uniform at the time. He was scheduled to work at Kennedy Airport later that night.
The NYPD's Hate Crime Task Force is investigating.
RELATED: NYPD Hate Crimes Task Force investigating two possible anti-Jewish bias incidents in Brooklyn
Police investigating two possible anti-Jewish bias incidents in NYC
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