As a schoolboy he decided he did not believe in God and stopped going to Sunday school aged 11.
He was told that his baptism cannot be deleted because it is a matter of historical record.
He then secured a "de-baptism" certificate produced by the National Secular Society (NSS), rejecting "superstitions" or the idea of original sin.
It reads: "I reject all its creeds and other such superstitions in particular the perfidious belief that any baby needs to be cleansed of original sin."
This week the church backed down and said the entry would be "corrected".
A representative of Southwark diocese told him: "I have spoken to the Archdeacon of Croydon and he has undertaken, in this particular case, to have it cross-referenced with the baptismal entry and pasted into the back fly-leaf of the relevant register at St Jude's Church." Dr Hunt, a former software engineer, said: "I am delighted that on this occasion the church are going to do what they said they would do."
He added: "It's about time that some of us stood up to be counted. I am hoping that others will follow my lead.
"It is important that we send a signal to the church and to the Government that an increasing proportion of the population don't place any faith in the various churches.
"The fact that we have 26 bishops in the House of Lords is an anachronism."
The NSS said an estimated 100,000 people had downloaded similar certificates from its website over the past five years, producing mock official versions and has had to order more parchment to meet demand.
Terry Sanderson, the NSS president, last month said the certificate was originally a "tongue in cheek" joke but conceded that the procedure was now being taken serious by a growing number of atheists.