Jeff Fairburn said he always intended to give a "substantial amount" of his triple-digit award to charity, and regrets not making his feelings public sooner.
The announcement comes after the company faced mounting pressure from politicians and some shareholders, such as the Church of England and the Methodist church.
Mr Fairburn said he "profoundly regretted" how the controversy surrounding his bonus had "eclipsed" Persimmon's strong performance.
He said: "Persimmon's success as a business and the uncapped nature of the scheme has meant that the value of these awards has become very large."
Defending his position, he said the introduction of the bonus scheme pre-dated his appointment and he had not sought out the bumper pay awards.
He added: "Once it became apparent that our outperformance would lead to a very significant award for me, I made plans to use a substantial proportion of the total to support the charities that are particularly important to me and my family.
"But, in what might be considered to be an old-fashioned approach, I believed that this was a personal matter and that I would be able to do this privately.
"It's now clear that this belief was misplaced and so I am making my plans public and recognise that I should have done so sooner."
Mr Fairburn became eligible for £40 million of the payout on New Year's Eve.
