The Besancon court overruled the Jura regional assembly, which had rejected the 48-year-old woman’s adoption plea.
France allows single people to adopt, but the government reiterated on Tuesday that it opposes adoption by same-sex couples.
The European Court of Human Rights backed the woman in January 2008.
The woman, identified only as Emmanuelle B, made the plea as an individual, but did not try to conceal her same-sex relationship – unlike many other homosexuals in France, the AFP news agency reports.
In their ruling in 2008 the European Court judges in Strasbourg decided that she was a victim of discrimination because of her sexual orientation.
They told France to pay her damages of 10,000 euros (£8,938) and 14,528 euros in costs.
The woman’s lawyer, Caroline Mecary, hailed Tuesday’s ruling as "a wonderful victory against homophobia".
Government spokesman Luc Chatel said "the government and the president have on several occasions expressed our position, which is that we are not in favour of the adoption of children by same-sex couples".
He said the government would take note of the legal ruling "and I think it should contribute to our thinking on the subject".