Speaking at the Church and Media conference in London last week, Chalke (above) said the person, "wants to have a renaming ceremony for who they really are".
Chalke also revealed that the ceremony will form part of a BBC documentary which looks at the Church's attitude to LGBT people.
"So that won't be controversial!", he quipped.
The renaming service will take place at Oasis Church Waterloo.
Explaining the decision, Chalke said: "This person was born intersex, which means they have both sets of sexual organs. Their parents made the decision to raise them as a girl and they had a physical operation. But of course they're wired differently!
"This guy says all he ever wanted to do was be a mechanic and play with cars. He lived the first 20 years of his life in utter guilt because his parents are committed Christians. He went to his parents because he was a girl and said I want to have a sex change and be a man.
"He thought they'd have a meltdown. His mum sat him down and said 'actually when you were born you were intersex and we chose for you to be a girl and I've always thought it was the wrong decision'."
Chalke also said he believes the acronym LGBT is "strange" because is joins together the "completely different worlds" of sexual orientation and sexual identity.
"Even if you're sure that Romans and 1 Corinthians and 1 Timothy condemn homosexual people that has absolutely nothing to do with the issue of transgender," he said.
Chalke has caused controversy in the past for his views on the Atonement and Scripture. In May this year, he became the first well-known Christian leader to announce his church would conduct same sex weddings.