Hayton has been in the position since 2016.
New Zealand Rugby League is currently going through a review following the Kiwis disastrous World Cup campaign last year.
NZRL Chairman Reon Edwards said "Alex has been a great servant to the game over the last decade and has seen through a number of major milestones in his time as both CFO and CEO."
"The discussions leading up to his decision to leave have been entirely amicable."
After 10 years' service with NZRL, Hayton said he's looking forward to a new challenge.
"We're starting a new World Cup cycle which coincides with our 2018-2021 strategic plan focused on grassroots development. The next CEO needs to be able to commit to the term of the cycle to see the plan through."
During his tenure as CEO, NZRL secured regular home Tests against Australia that start this year, new NRL funding for the NZRL's Talent Development Programme, and an increased profile in the women's game.
Securing the hosting rights for 2017 Rugby League World Cup in New Zealand was definitely "a career highlight", said Hayton, "with the passion and emotion at the games creating some of the best sporting experiences in New Zealand."
While unable to comment on the upcoming Review Panel's findings, Hayton said he was prepared to accept his responsibility in the team's disappointing performances.
The New Zealand Rugby League Board will release the recommendations from a comprehensive review of the Kiwis' 2017 Rugby League World Cup campaign within the next fortnight.
Edwards said a recruitment process would begin immediately.
Experienced company CEO and director Hugh Martyn - will take up the role of Acting CEO on a part-time basis.