Mr. Filner was spotted leaving City Hall with boxes Wednesday night. He formally will resign following a closed session of the City Council on Friday, the report said.
More than a dozen women have come forward claiming sexual harassment and unwanted sexual advances by the mayor.
Mr. Filner apologized and entered a treatment program for a couple weeks before beginning an outpatient program.
During three days of negotiations, officials reached a deal. Once Mr. Filner resigns, San Diego city government will enter a period of interim leadership, and council President Todd Gloria will take on the role of acting mayor, NBC 7 News reported.
There could be at least one primary special election within 60 to 90 days, the station said.