Kenyon, 55, will continue to serve as a non-executive director and will represent the club on various UEFA and European Clubs' Association committees, said a statement on the club's website.
Kenyon, formerly head of sportswear firm Umbro, made his name at Manchester United, where he spent six years, three as chief executive, before leaving to join Chelsea in February 2004 following the takeover of the club by Roman Abramovich.
Since then, backed by the Russian's huge investment, Chelsea have won the Premier League twice - their first championship titles since 1955 - plus the FA Cup and League Cup twice each.
They reached the Champions League semi-finals five times in six seasons, losing in the final of Europe's leading club competition to Manchester United on penalties in 2008.
COMMERCIAL DEALS
Kenyon was instrumental in the club's two record commercial deals - a shirt sponsorship with Samsung, the most lucrative in Premier League at the time and which has been renewed for a higher sum, and a record kit supplier deal with adidas.
"I am extremely proud of my time at Chelsea and of the friendships I have forged with everyone here," Kenyon said in a statement on Wednesday.
"I have been in football for 15 years and I can say with great certainty and pleasure the experience at Chelsea is one of the best I have had.
"When I joined Chelsea it was an incredible challenge and together with all the staff, the players, the board and Roman, I think we have really built a club, in a relatively short space of time, that can be in the forefront of European football for many years to come. That is a major achievement.
"I am also delighted that our relationship is not ending and I can continue to make a contribution to keeping Chelsea in that position and to go back to visit friends.
"I intend to take a little time off before considering what I do next but I am certain I have at least one major challenge left in me."
Chelsea chairman Bruce Buck added: 'Peter has done a fantastic job for Chelsea in the last five-and-a-half years and has been absolutely central to the success on and off the field we have had during that time.
"Without his football knowledge and business acumen Chelsea would not be where we are today."
