In a statement, Congresswoman Madeleine Bordallo says she has accepted John Whitt's resignation with immediate effect.
Mr Whitt was arrested in Maryland in April on allegations of second-degree assault and unwanted sexual contact, and charges were filed in a local court this week.
Ms Bordallo says she has a responsibility to represent and advocate the people to the best of her abilities, and the pending allegations against Mr Whitt could detract from carrying out those responsibilities.