Yusuke Hasegawa will succeed Yasuhisa Arai as the head of Honda's Formula 1 programme ahead of the new season.
Honda, which has struggled to master F1's new turbo hybrid engine technology since its return last year, said the move was part of an annual organisational change.
Arai, 59, reaches Honda's management retirement age of 60 next year.
Hasegawa will assume his role on 1 March with Arai becoming senior managing officer at Honda's Sakura HQ.
He will continue to attend some grands prix through this year as Honda completes its handover process.
The F1 programme, which is operated as part of Honda Research and Development, will be overseen by a new role at the parent Honda Motor Company.
This supervising officer will be Yoshiyuki Matsumoto.