The airline began a review of their uniform policy last year, after Heathrow check-in worker Nadia Eweida was banned from wearing a small cross on a chain. Miss Eweida refused to remove the cross and was on unpaid leave for three months while the company reassessed their policy.
Critics pointed out that the company did allow staff to wear turbans and Muslim headscarves.
The airline argued that these could be visible as part of a uniform as they could not be worn underneath clothing. Many church leaders and politicians condemned this distinction.
Asked at a conference by BA's Martin Broughton how they should handle the issue, Prime Minister Tony Blair advised them to "do the sensible thing".
During the review, BA consulted staff and customers, examined the uniform policies of other organisations and canvassed the opinions of the Church of England, the Catholic Church and the Muslim Council of Britain.
British Airways chief executive Willie Walsh said: "Unintentionally, we have found ourselves at the centre of one of the hottest social issues in current public debate.
"Most of those consulted felt that a lapel pin was an acceptable and reasonable option. For the majority of our staff, this was the preferred option.
"However, some respondents believed that limiting the change to a pin would not satisfy all Christians.
"Comparisons were made between the wearing of a cross around the neck and the wearing of hijabs, turbans and Sikh bracelets. For this reason, we have decided to allow some flexibility for individuals to wear a symbol of faith on a chain."
The Archbishop of Canterbury, Dr Rowan Williams, has welcomed the move. He said: "I am grateful that BA has listened to the deep concerns that have been expressed about this issue and that their change of policy now allows Christians to wear crosses openly.
"Important issues have been raised. This is a positive and constructive outcome."
At the height of the controversy, Dr Williams had said that the Anglican Church, which is an investor in BA, would "rethink its whole attitude" to the airline.
At the height of the controversy, Dr Williams had said that the Anglican Church, which is an investor in BA, would "rethink its whole attitude" to the airline.