Councillors passed the application to build the stadium, clubhouse, pitches and car parking at Ronald Johnson playing fields in Moston, Manchester, for 2012-13.
FC United was set up by Manchester United fans disgruntled by the Glazer takeover in 2005.
The approval is subject to the signing of a section 106 agreement, to include community use of the site, plus a travel plan being submitted and reviewed, and the provision of off-site parking.
Councillor Paul Murphy, who represents Moston on the city council, said: "If the application is approved, it will bring much needed investment to Moston - close to £4m.
"It will also bring sporting facilities for the young people of Moston and the surrounding areas, which again is much needed and will be developed in a professional way."
FC United, which is owned and run by its members, currently plays at Bury FC's Gigg Lane.
It chose the Moston site to be near to Newton Heath, Manchester United's original name.