About 100 delegates to the national assembly of the United Protestant Church of France (EPUdF) on Sunday voted 94-3 to allow its 500 pastors to celebrate same-sex marriages.
Pastors who oppose the move will not be obliged to do so, however.
The church claims to have 110,000 active members and 400,000 people who sometimes attend its functions.
The much smaller Popular Evangelical Mission has already authorised a ceremony of "prayer and liturgical welcome" for homosexual couples.
Traditionalist Catholics played an active role in massive demonstrations against the Socialist government's gay marriage bill, which was passed two years ago, and the Vatican has been holding off on accepting a gay ambassador from France, apparently partly because of the law.