Both the FTC and a large group of state attorneys general, led by New York, filed lawsuits against Facebook in December before the U.S. District Court for the District of Columbia alleging violations of antitrust law. The company was accused of using its dominance to crush smaller rivals.
The state attorneys general requested last month that the cases be consolidated. Facebook objected to the consolidation, saying it was "premature and unnecessary" but did not object to the same judge hearing both cases.
Judge Chris Cooper, who had been assigned the FTC's case, said in a minute order on Tuesday that he was asking for it to be re-assigned to Judge James Boasberg, who is hearing the similar case filed by state attorneys general.
Boasberg was nominated to the court by President Barack Obama, and is also presiding judge on the United States Foreign Intelligence Surveillance Court, which considers surveillance requests from U.S. law enforcement.
(Reporting by Diane Bartz; Editing by Dan Grebler and David Gregorio)