Acting Superintendent Patrick Hallinan is taking the post permanently, Army Secretary John McHugh told The Washington Post.
McHugh also said staff will be trained at the Department of Veterans Affairs to improve the vast cemetery's operation.
In June, the Army inspector general revealed more than 200 discrepancies between burial maps and grave sites and some urns that were dumped in a dirt pile. Some remains also have been buried in the wrong plots.
Hallinan replaces John Metzler Jr., who was superintendent from 1991 until he was dismissed in June along with his deputy, Thurman Higginbotham. Investigators found that under their leadership, Arlington paid millions to digitize its paper records with nothing to show for the effort.
Updating antiquated paper records, along with fixing the discrepancies, are top priorities, Hallinan said.
A bill introduced in the Senate last month calls for a study into transferring the cemetery from the Army to the VA.