Attorneys for the PETA had asked the judge to free five orcas from SeaWorld.
Kasatka, Corky and Ulises are at SeaWorld in San Diego, while Tilikum and Katrina are in Orlando, Fla.
But on Wednesday, the judge ruled that the whales had no standing to seek the same constitutional rights as people.
"The only reasonable interpretation of the 13th Amendment's plain language is that it applies to persons, and not to non-persons such as orcas," U.S. District Judge Jeffrey Miller wrote in his ruling.
"Both historic and contemporary sources reveal that the term 'slavery' and 'involuntary servitude' refer only to persons," the judge added.
Miller said the goal of protecting the orcas was "laudable," but using the 13th Amendment was not the proper way to do so.
PETA announced plans to sue SeaWorld several months ago, claiming that it was, "...keeping orca whales in slavery."
"All five of these orcas were violently seized from the ocean and taken from their families as babies," PETA President Ingred Newkirk said in a prepared statement.
SeaWorld attorneys asked the court to dismiss the lawsuit, saying it was a publicity stunt for PETA.
PETA has vowed to regroup in the wake of the decision.
"Today's decision does not change the fact that the orcas who once lived naturally wild and free, are today kept as slaves by SeaWorld," PETA spokeswoman Colleen O'Brien said in a statement.