Ezra Chiloba, CEO of Kenyan Independent Electoral and Boundaries Commission (IEBC), said on Friday he was taking three weeks of leave.
Opposition demanded that Chiloba must be fired before a repeat presidential election scheduled for October 26.
The first presidential vote in August, which gave victory to Kenyatta, was annulled because of procedural irregularities.
Chiloba said he had taken a personal decision to take leave in light of the opposition’s demands, without giving more details.
He said all arrangements were in place for the election, as ordered by the supreme court.
“This is the first time I‘m taking leave since my son was born. He turns two years (old) in two weeks’ time,” he was quoted as saying.
The court annulled the first election, held in August and in which incumbent Uhuru Kenyatta was declared winner, over procedural irregularities.
The opposition, led by Raila Odinga, has said it will boycott the rerun unless several demands, including the sacking of Chiloba, are met.
Odinga met the chairman of the IEBC board, Wafula Chebukati, on Thursday and later told reporters that if there were serious consultations and serious reforms, the opposition could review its boycott.
The board has said the election will go ahead and Kenyatta has insisted the vote must be held.
On Thursday, the president snubbed an invitation to meet Chebukati, saying he would instead spend the time campaigning.