The Vasa Real school which offers classes in Jewish studies and Hebrew was emblazoned with pink and blue swastikas and anti-Semitic slogans, including "disgusting Jews" and the white supremacist insignia "1488," school authorities said.
"During the night several walls were sprayed with racist markings," police added in a statement.
"Horrible and unacceptable," tweeted the local council's school director Johanna Engman, as the graffiti was removed on Monday morning.
Swastikas were also painted on a nearby high school in Stockholm with a high proportion of ethnic minority students, school authorities said.
"It's particularly sad because many come to our school precisely because we reflect how Swedish society looks today," a spokeswoman for Cybergymnasium high school, Marlene Terkowsky, told newspaper Metro.
Police said meanwhile that two women and two men were injured late Saturday in the southern Swedish city of Malmo when a fight broke out between left wing militants taking part in a feminist march and members of the far right Party of the Swedes.
In January, a Stockholm mosque was also targeted by extremists who painted black swastikas on the entrance.
Members of a Swedish Neo-Nazi group are currently on trial in Stockholm for attacking a peaceful anti-racist demonstration in a Stockholm suburb which was held to protest against an uptick in swastikas being painted on walls in the area.