"My 13-year-old daughter was on the way to school and she saw that one of the entrances was totally bombed by graffiti," Calle Nathanson told The Local.
The scrawlings included swastikas, the words "Jewish swine" and "disgusting Jews", and the number 1488, which is a symbol for white power and the Nazi greeting Heil Hitler.
Nathanson tweeted several pictures of the graffiti, writing that it was "completely incomprehensible and unacceptable".
"I am crying," he wrote on the micro-blogging service.
Min dotter kommer till Vasa Real på måndagsmorgonen o möts av svastikor o orden "judeäckel" - det får vara nog nu! pic.twitter.com/Ya9OSj1mff— Calle Nathanson (@CalleNathanson) March 10, 2014
"That's enough now!" wrote Nathanson on Twitter.
The central Stockholm high school has more than 800 pupils from grades five to nine, when the children are between 11 and 15. At high-school level, there are three classes with Jewish children who study the Swedish curriculum but also study Hebrew and Jewish studies, according to the Vasa Real website.
Nathanson said his teenage daughter did not really understand the significance of the messages.
"She was curious... she said to me that she thought it was just drunk and stupid boys in the night. It's hard to understand. But me, I know that there's a wave of Nazism spreading through Europe right now. Greece, Hungary, Ukraine... this is populist parties emanating from fascism. And it's happening here. Especially in Stockholm," he told The Local.
He pointed to examples including the recent demonstrations in Kärrtorp, southern Stockholm, and the Nazi graffiti scribbled on the doors of the Stockholm mosque last year.
"The fact that they targeted a school with Jewish kids is a sign for me that they're really organized. They know exactly what they're doing," he told The Local. "It's incredible that (Swedish security police) Säpo doesn't work efficiently with this issue... they must start taking it seriously."
The school was closed for the morning while staff members met and discussed how to move forward. Cleaners, meanwhile, worked to remove the scrawlings. The school said in a statement that the incident had been reported to police and was under investigation.
Lena Posner-Körösi, head of the Jewish Community Association of Stockholm, told the TT news agency that she had received several calls from parents at the school throughout the day.
"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," she said.
"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."