Nadia Eweida took her case to the ECHR after BA made her stop wearing her white gold cross visibly.
The court said BA had not struck a fair balance between Ms Eweida's religious beliefs and the company's wish to "project a certain corporate image".
It ruled the rights of three others had not been violated by their employers.
But they said Ms Eweida's rights had been violated under Article 9 of the European Convention on Human Rights.
The four Christians had brought cases against the UK government for not protecting their rights but ministers, who contested the claims, argued that the rights of the employees were only protected in private.
Ms Eweida, 60, a Coptic Christian from Twickenham in south-west London, told the BBC she was "jumping with joy" after the ruling, adding it had "not been an easy ride".
British Airways said its uniform policy was changed in 2007 to allow Miss Eweida and others to "wear symbols of faith" and that she and other employees had been working under these arrangements for the last six years.