A bill sent to the Senate by the House of Representatives extends FAA operating authority through the middle of September. The bill also includes a provision to cut $16.5 million in air service subsidies for rural communities. Those cuts are part of a Republican push to rein in spending.
The Senate version was expected to negate the cuts.
Thirteen rural communities would be affected by the provision.
"This is a tremendous victory for American workers everywhere," Transportation Secretary Ray LaHood said in a statement.
President Obama released a statement Thursday afternoon: "I'm pleased that leaders in Congress are working together to break the impasse involving the FAA so that tens of thousands of construction workers and others can go back to work. We can't afford to let politics in Washington hamper our recovery, so this is an important step forward.
The Associated Press contributed to this report.