In November last year Nottingham Employment Tribunal dismissed all claims made by the vicar.
He married Laurence Cunnington last April but had his right to officiate removed by the then acting Bishop of Southwell and Nottingham Rt Revd Richard Inwood following the wedding.
The clergyman then had a job offer as a chaplain for Sherwood Forest Hospitals Trust withdrawn, which he claims was caused by the Church of England discriminating against him because of his sexual orientation.
But the tribunal ruled "the constitutional convention means that the State cannot impose same sex marriage upon the Church".
In their ruling the tribunal panel said the case had "profound implications" for the Church of England.
It said that Canon Pemberton had been warned of the consequences by the Church if he went ahead and entered a gay marriage.
Bishop of Sherwood Rt Revd Anthony Porter wrote to him saying it would not be "appropriate conduct".
Canon Pemberton replied to the bishop saying the Church's teaching was "of doubtful legality".
"It is a core part of the qualifying of a priest for ministry within the Church that he confirms to Canonical Obedience," the ruling said.
He has now taken his case to the Employment Appeal Tribunal in London.
The hearing is scheduled to last two days.