Washington had tried to block European Union plans to levy the emissions tax, saying they were invalid and that plans for an emissions tax on airlines must be dealt with by the International Civil Aviation Organization.
However, the European Court of Justice ruled on Wednesday that the taxes were legal, the BBC reported.
The United States, Canada and China had all opposed the plan.
"We are disappointed by the decision of the court," U.S. State Department spokeswoman Victoria Nuland said.
"Our message to the European Union has been very, very consistent: that there are mechanisms in international aviation in ICAO for addressing the question of greenhouse gas emissions and that's where these things should be talked about," she said.
U.S. airlines argue the emission taxes go against the Open Skies Agreement, which allows airlines to fly between any EU country and any point in the United States.
The European Court of Justice rejected that argument.
"Application of the emissions trading scheme to aviation infringes neither the principles of customary international law at issue nor the Open Skies Agreement" across the Atlantic, the ECJ said.