The House approved the measure Friday on a 361-41 vote, one day after the Senate agreed to the bill. The action came with lawmakers streaming toward the doors for a week-long spring recess.
The Federal Aviation Administration has furloughed the controllers as part of the government-wide, $85 billion spending cuts called the sequester.
Republicans are accusing the Obama administration of using the controller furloughs to put political pressure on Congress to roll back all the cuts. Airline delays have infuriated travelers and caused headaches for lawmakers.
Democrats largely went along with the bill but said all the cuts should be lifted.