Most Rev Justin Welby said he would put his personal opinion to the side when the Bill, to allow the Prime Minister to start the process of leaving the EU, comes to the chamber.
Whilst doing a radio phone in on LBC he was challenged by Judith from Whitstable who demanded to know why he "interfered with the referendum vote".
Archbishop Justin denied interfering and said that whilst he wrote a blog saying he was voting remain he did not tell others to.
Judith said she had refused to go to church since because the clergyman backed remain.
He replied: "Within the Church we have loads of different views about this... I obviously accept that we voted leave and when it comes to the vote in the House of Lords I'll be supporting the Brexit Bill.
"But I would say to her it's about Jesus Christ, it's not about what a particular archbishop says or their personal opinions".
He said that Judith "may well be right" when she said it was wrong for him to say how he would vote.
