Revd Andrew Foreshew-Cain said he was "feeling daunted, elated and ready", after the results for the Diocese of London were announced.
He was the first serving vicar to reject the Church's rules and marry his same sex partner in 2014, after the House of Bishops ordered Anglican clergy in England not to enter gay marriages.
At the time officials said it would not be "appropriate conduct".
In a tweet announcing his election he said there was "hope for a kinder more compassionate Church".
Revd Foreshew-Cain is the vicar at St Mary with All Souls church in Kilburn, and St James in West Hampstead.
The General Synod is generally considered the parliament of the Church of England.
It makes major decisions within the Church, including, recently, allowing women to become bishops.
Other dioceses will announce their members of the Synod later in the year.
OK. Having been in shock I am now realising I have been elected to General @synod of the CofE. Feeling daunted, elated & ready. NO SURRENDER
— Andrew Foreshew-Cain (@churchnw6) October 12, 2015
Andrea Williams, chief executive of Christian Concern and a member of the Church of England's General Synod 2010 - 2015, said: "Last year, Andrew Cain ignored biblical teaching and the clear instruction of the House of Bishops and entered into a same-sex marriage.
"Andrew Cain's ongoing activism should no longer be tolerated. His actions are designed to undermine the Church and her teaching on marriage. His election to General Synod cannot be allowed to stand and he should be swiftly removed from church leadership."
Meanwhile, Canon Jeremy Pemberton, another priest who entered a gay marriage, was unsuccessful in his bid to be elected in the Diocese of Lincoln.