It's a defeat for families dissatisfied with how they fared before a special no-fault vaccine court.
The court voted 6-2 against the parents of a child who sued the drug maker Wyeth in Pennsylvania state court for the health problems they say their daughter, now 19, suffered from a vaccine she received in infancy.
Congress set up a special vaccine court in 1986 to handle such claims as a way to provide compensation to injured children without driving drug manufacturers from the vaccine market, and according to Justice Antonin Scalia, the idea was to create a system that spares the drug companies the costs of defending against parents' lawsuits.
Justices Ruth Bader Ginsburg and Sonia Sotomayor dissented.
The American Academy of Pediatrics praised the high court's decision.
"Childhood vaccines are among the greatest medical breakthroughs of the last century," said Dr. Marion Burton, the group's president. "Today's Supreme Court decision protects children by strengthening our national immunization system and ensuring that vaccines will continue to prevent the spread of infectious diseases in this country."
The vaccine court has paid out more than $1.9 billion to more than 2,500 people who claimed a connection between a vaccine and serious health problems.
Justice Elena Kagan took no part in the case because she had worked on it while serving in the Justice Department.
The Associated Press contributed to this report.