The Radio Advertising Clearance Centre (RACC) refused to allow the advertisement, made by Premier Christian Radio and intended for broadcast in the run-up to the General Election last year.
The advert quoted surveys showing that 60% of active Christians are being increasingly marginalised in the work place.
“We are concerned to get the most accurate data to inform the public debate. We will then use this data to help make a fairer society," it said.
However the RACC refused to let the advert air, claiming that it had a political objective.
Premier was granted a judicial review in June but it was challenged by the RACC. Today's ruling means the station's legal challenge can go ahead.
The judge indicated that he would like the case expedited as this is an issue of great importance that involves the freedom of expression.
Premier said it should have the right to obtain information about listener’s experiences of religious marginalisation as it could subsequently be used to inform debate and lobby the government for a change in law.
Premier's chief executive, Peter Kerridge commented: “This has been a long hard fight but, at last, we have the right for a judicial review to clarify the law in matters of religious expression."
Solicitor Tom Ellis, acting for Premier Christian Radio, said: “This is an important case for Christians and their expression of religious views. Airing this particular advert will allow people to do just that and the information gathered can then be used by equal opportunity groups in future debate and to further the cause of religious equality.”