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.