Andrew Foreshew-Cain announced on Sunday he is to leave his post at St Mary with All Souls in Kilburn and St James in West Hampstead, north London.
In a letter to parishioners, the 53 year old said: "I am not giving up on being a Christian. I am having my ability to function as a priest denied."
Foreshew-Cain also claimed a Church of England ban on clergy entering same-sex marriages harmed both the LGBT community and the church's reputation.
Speaking with the Guardian, he said: "In the normal course of things, I would look for a job in the area. But I am on blacklist. I can't carry on being a priest because the institutional homophobia of the church makes it impossible.
"I am sure lots of parishes would give me a job quite happily, but it is finding a bishop who would be willing to take the risk of licensing me to that parish."
Foreshew-Cain, who is moving to Manchester after nearly 30 years working for the Church of England, also said gay and lesbian clergy are "barely tolerated rather than fully accepted and celebrated".
A Diocese of London spokesperson told the Guardian: "Fr Andrew Foreshew-Cain is currently a member of the clergy in the diocese of London.
"We understand that he has plans to move to Manchester for personal reasons but the diocese has not received his resignation at this time."