"Jewish swine," "disgusting Jews" and swastikas were among the things spray-painted onto the walls of the Vasa Real high school. Vandals also scrawled the number 1488, a symbol associated with the white power movement and the Nazi greeting Heil Hitler.
Vasa Real is not an exclusively Jewish school, but offers Hebrew and Jewish Studies classes to its Jewish students in addition to the Swedish curriculum.
In Sweden, anti-Semitic incidents have been on the rise. The most recent high profile attack was an assault on anti-Nazi protesters by neo-Nazis in a Stockholm suburb in December.
Monday's incident drew attention to the increasing sense of anti-Semitism and the influence of far-right political parties and groups in Europe, like Sweden's national socialist Party of the Swedes and Greece's Golden Dawn.
"This is the first time there has been anti-Semitic graffiti aimed at Vasa Real and its Jewish students, but if you piece together everything else that's happening, you'll see that it's more than just individual coincidences," Lena Posner-Körösi, head of the Jewish Community Association of Stockholm, was quoted as saying.
"We have an extremely worrying development both in Sweden and Europe where right-wing groups are winning power," she added. "This is a very uncomfortable situation we are facing, 70 years after the Holocaust."
The school said in a statement that the incident had been reported to police and was under investigation.