An overwhelming 94 out of 100 delegates of the "Union of Protestant Churches in France" (EPUdF) voted to allow gay marriage to be blessed. Only three voted against.
However, vicars who are opposed to the practice will not be forced to bless gay couples in their churches.
Same-sex marriages were legalised in France in May 2013.
In secular France, marriages in church have to be proceeded by a civil ceremony in a town hall.
The EPUdF, the main protestant group in France, whose Christians are mainly Catholic, claims to have 110,000 active members from a community estimated at around 400,000 believers.
It is thought to be the fourth biggest religious grouping in the country, after Catholics, Jews and Muslims, although precise figures are hard to come by as France does not collect statistics on religion.
The vote in France came as Ireland prepares to hold a referendum on legalising same-sex marriage this week.
And on Saturday, the Church of Scotland voted to allow the ordination of ministers in same-sex civil partnerships in a breakthrough for gay rights.