The chamber voted 52-40 for Dickson to head the agency as it faces scrutiny of its oversight after recent two Boeing 737 Max crashes overseas killed nearly 350 people.
Wednesday's was a rare party line vote for the job, the nominees for which typically receive near-unanimous support from the Senate. Sen. Maria Cantrell, D-Wash., cited an "ongoing case" regarding whistle-blower retaliation at Delta as a source of concern for Dickson's confirmation.
Delta came under investigation by the FAA after Dickson grounded a pilot for psychiatric evaluation after she reported safety concerns to him and other executives. She has since returned to flying for the airline.
"We've never had a partisan vote on an FAA nominee in the past, and I believe that we should have found consensus on a nominee for the FAA, given all of the concerns the public has about flying safety," she said on the Senate floor.
The FAA has been without a permanent administrator since Michael Huerta's departure in January 2018. Daniel Elwell took over as acting administrator.