The governing body is meeting for four days in York.
The agenda includes a suggested change on the church's stance on conversion therapy for people experiencing same-sex attraction.
Synod member Rev Canon Jonathan Ford is concerned it's a no win situation.
Speaking to Premier, he said: "If we don't vote against therapy we'll be seen by some to be supporting the worst forms of these therapies, if we vote for it there may well be a witch hunt.
Discussions on how to make the church more welcoming to transgender people will also take place.
The first point of business on Friday was a debate introduced by the Archbishops of York and Canterbury looking at the role of the Church after the election.