The New York Times reports that the Federal Election Commission found that the Harlem Democrat accepted campaign contributions beyond the legal limit when he leased the apartment at a price below market rate.
City and state guidelines require rent-stabilized apartments be solely used as a primary residence.
Rangel moved his campaign office out of the apartment soon after the leasing arrangement became public.
His spokeswoman told the Times that the agreement to pay the civil fine was not an admission of guilt.
The 81-year-old congressman announced last week that he'll run for a 22nd term. He was convicted on House ethics charges in 2010.
Copyright 2012 The Associated Press.