The attack happened at around 9.30pm in the Alt-Treptow neighbourhood, police report.
According to the 21-year-old victim, three men of Arabic appearance reacted to his kippah - a religious cap worn by Jewish men - and then started to insult him.
The men then went on to kick and punch him before running away from the scene.
The young man was lightly injured but did not need to go to hospital.
Instances of anti-Semitic crime are on the rise in Berlin, as are hate crimes of various forms, according to a report published in March.
Hate crime monitoring groups ReachOut and Berliner Register reported at the time that there were 320 incidents of attacks motivated by anti-Semitism, racism, or homophobia in 2015, up from 179 in 2014.
Twenty-five of the attacks last year were connected to anti-Semitism, compared to 18 the year before.
Most victims of anti-Semitic crime are wearing kippahs at the time of the attack, Tagesspiegel reports.
In one such attack, in October 2015, four men of Middle Eastern appearance insulted and spat at an Israeli travelling on the city’s underground system.
Jewish leaders have expressed concern that refugees arriving from the Middle East could pose a danger to Jews in Germany.
Salomon Korn, president of the Frankfurt Jewish community, warned in January that many refugees had grown up in environments rife with anti-Semitism.
Interior Minister Thomas de Maizière has said previously that he was more worried about home-grown extremists than anti-Semitism among arriving refugees.