Rev Rola Sleiman had been invited by the Church of Scotland to attend its General Assembly, an annual meeting which gets underway again in Edinburgh on Saturday.
The 42 year old, who is currently a parish minister in the Lebanese city of Tripoli, said: "The mentality they have that we are eagerly wanting to leave our country using fraud reasons is humiliating".
So disappointing to hear this today! Quite a number of times this year visits to the Church of Scotland have been stopped by this... https://t.co/uI8NvmBvoE
— Kirk Youth Moderator (@nyamoderator) May 15, 2017
Rev Sleiman received a letter saying her visa application had been unsuccessful because the UK government was not convinced about claims concerning her incomes or that her expenses during the trip would be covered.
The note from the UK Visas and Immigration department said: "I am not satisfied that you intend to leave the UK at the end of your proposed visit. Or that you will not live in the UK for extended periods through frequent or successive visits.
"Furthermore, I am not satisfied that you are genuinely seeking entry for a purpose that is permitted by the visitor routes and you will not undertake any prohibited activities."
The decision comes despite the Church of Scotland confirming that Rev Sleiman's costs would be covered during the planned eight-day stay.
Speaking with Premier, Very Rev Dr John Chalmers, the Principal Clerk to the General Assembly, said: "We were very much hoping to have her as a representative to bring some insights to us from a very significant part of the world.
"She was going to be participating in the assembly services at St Giles on Sunday so it's a big dissapointment at this stage but we are in touch with the Home Office and with the Foreign and Commonwealth Office in so far as they might be able to do something about this, even at short notice."
Rev Sleiman, who holds a Syrian passport, was due to represent the National Evangelical (Protestant) Church of Syria and Lebanon at the Church of Scotland's General Assembly.
The Church of Scotland is calling upon the UK Government to review and reverse its decision.
The Home Office told Premier it did not "routinely comment on individual cases" but "each application is considered on its individual merits based on the evidence provided and in line with the UK's Immigration Rules."
Claim here to listen to Very Rev Dr John Chalmers speaking with Premier's Ian Britton: