The court ruled that Örebro University in central Sweden was guilty of gender discrimination and must pay each of the women 75,000 kronor ($11,145) in damages and cover their court costs.
The university was not however required to grant the women admission.
The three women, now aged 23, 23, and 21, had applied to the school’s Health Promotion programme in 2005, but were denied admission. Three men who had lower grades were admitted.
“The verdict is as pleasing as it is important,” said the women’s legal representative Gunnar Strömmer.
“It makes it clear that it is not permissible to discriminate against applicants to a third level institution on the basis of gender,” added Strömmer, who heads the non-profit public interest law organization Centrum för Rättvisa (Centre for Justice).
University officials told the Örebro district court that it had applied affirmative action rules because it wanted to increase the number of male students in the programme as men were underrepresented.
But the court ruled that the university had discriminated against the women, as affirmative action rules only allow the university to admit the men instead of the women if they all had similar grades.
The university has not yet decided whether it will appeal the verdict, according to Swedish news agency TT.
The Swedish government has allowed universities to apply affirmative action since 2003. About 60 percent of university students in Sweden are women.