Most Revd Justin Welby made the comments at the launch of the Religious Liberty Commission, a joint venture by several UK based Christian anti-persecution organisations set up to lobby the government into appointing a Special Envoy for Freedom of Religion or Belief to challenge religious persecution around the world.
Archbishop Justin appeared to suggest that accepting criticism of religion was as important as being able to freely practice one's faith in public.
Speaking at the event in the Chapel of St Mary Undercroft in the Palace of Westminster on Wednesday, he said: "Well, if we believe in freedom of choice, if we believe in freedom of religion what is good for one is good for all.
"We must speak out for others persecuted for their beliefs whether it be religious or atheistic.
"Taking responsibility for someone else's freedom is as important as my own.
"It is as much the right of Stephen Fry to say what he said and not to be abused improperly by Christians who are affronted as it is the right of Christians to proclaim Jesus Christ.
"That is his freedom to choose that is given to us in creation."
Last week, the actor and TV presenter launched a rant against God saying he is mean minded and stupid, which has had over two million views on YouTube.
In an interview with Irish broadcaster RTE, Mr Fry said: "I'll say 'bone cancer in children - what's that about? How dare you. How dare you create a world in which there is such misery that is not our fault. It's not right; it's utterly, utterly evil.'
The Evangelical Alliance, Christian Solidarity Worldwide, Open Doors (UK) and Release International, through newly formed Religious Liberty Commission have also called on church leaders to formally adopt the International Day of Prayer for Persecution Christians.
Speaking to the media after the event, the Archbishop of Canterbury also admitted that Saudi Arabia needed to 'improve' its record on human rights, which, he said, included religious freedom.
Last month Archbishop Justin caused controversy after openly supporting the UK's decision to lower flags on state buildings following the recent death of Saudi Arabia's King Abdullah, despite the state's appalling record on human rights.
The Archbishop refused to be drawn on the issue of flags, suggesting it was a " matter for the government", however he agreed the country had to improve its human rights record, he said: "We need to say clearly, that that is one country among many where there needs to be a very very significant move around all human rights, including freedom of religion."
Most Revd Justin Welby:
