Revd Clive Larsen (above left), 60, led St Agnes Church in Stockport until his resignation on Friday.
Mr Larsen, who is previously married and has two daughters, celebrated his wedding in the church on Sunday.
He told the Sunday Times: "If this is something you want to do, you have to pay the price and leave the church.
"I am aware of two other clergy who have had [same-sex marriages] and the church has made life very difficult for them."
Church of England rules ban clergy from marrying partners of the same-sex and bishops are required to discipline those who break the rules.
The Church currently affirms marriage as between a man and a woman only, but has recently hosted "shared conversations" about the topics where bishops, clergy and laity have explored each other's varying opinions on the topics in small, private groups.
The Diocese of Manchester said: "The Revd Clive Larsen tendered his resignation from his post in Reddish in Manchester Diocese some time ago.
"That resignation was effective from 22nd July. Clive does not have permission to officiate as a priest in the Diocese, nor has he sought to apply for it.
"We can confirm that Clive has been made aware of the House of Bishops Pastoral guidelines in relation to same sex marriage."