"The delay in desegregation has deprived generations of students of the constitutionally guaranteed right of an integrated education," Brown wrote in a 96-page opinion .
Merging black and white schools was a common desegregation method in the 1960s and 1970s, and the opinion is a reminder that desegregation lawsuits never ended in some places.
Gary Orfield, who directs the Civil Rights Project at the University of California, Los Angeles, said that remedies like Brown's are unusual today.
"The court concludes that the continued operation of East Side High and D.M. Smith as single-race schools is a vestige of discrimination and that, therefore, a plan which allows such continued operation must be rejected," the judge wrote.
Federal officials have called for rebranding schools, more academic options and a community advisory panel to guide the transition.
The school district presented expert testimony that white parents were likely to flee to private schools.
