Nadia Eweida, 58, had appealed against an employment tribunal decision that cleared BA of religious discrimination over its policy, which changed following a furore over her case in 2006.
Eweida, a part-time check-in assistant since 1999, complained about anti-Christian bias after BA introduced a new uniform in 2004 and prohibited the wearing of any adornment around the neck.
When she refused to cover up her crucifix, she was sent home and remained unpaid from September 2006 until February 2007.
At that point "a storm of media attention" led BA to reconsider its uniform policy and to allow staff to display a faith or charity symbol with the uniform, said judge Stephen Sedley.
Eweida returned to work, but claimed she was due some STG120,000 ($A210,000) in damages and lost wages.
But the judge said BA had been justified in imposing a ban, however much it conflicted with an individual's religious beliefs.
The case reflects "problems which can arise when an individual asserts that a ... practice adopted by an employer conflicts with beliefs which they hold, but which may not be shared but may be opposed by others in the workforce.
"It is not unthinkable that a blanket ban may sometimes be the only fair solution," he said.
Rights group Liberty said it was "startling" that it was not discriminatory to ban someone from wearing a crucifix, on the grounds that Christians do not "generally" consider it a requirement of their religion.
"This is a disappointing judgment that will do little to build public confidence in equality laws protecting everyone," said Corinna Ferguson, the legal officer from Liberty who represented Eweida.