The United States has been supporting the French military's operations in northern Mali by providing refueling services for French forces and airlift support for French and Chadian forces.
Obama issued a memorandum to the State and Defense departments Monday advising them of his directive to use the $50 million. The State Department already had notified Congress of Obama's intent to tap Pentagon funds.
A White House national security official said France is reimbursing the U.S. for fuel.
The U.S. has supported French efforts to knock out terrorist sanctuaries in Mali, but has avoided direct involvement.