Rigg joined the Craven Cottage side at the start of 2015 following a two-year spell with the Football Association.
He previously worked at Manchester City and QPR as a technical director.
Rigg worked closely with Fulham's scouting team, but the Whites said his departure would not affect their plans for the January transfer window.
"Mike made many solid contributions to our club and I know he will be up to the next challenge in his career," chairman Shahid Khan said.
Mike Rigg has left his position as chief football officer at Fulham after agreeing to "cordially part ways" with the Championship club.