But he handed in his notice after a disagreement with the Walsall chairman Jeff Bonser over future transfer funds.
"The timing of my departure will give the club the maximum opportunity to bring in a new Manager, and to give him the chance to bring in his own players for next season," he said.
"I am proud of what we have achieved over the past two years. Winning the League Two Championship was a very special moment for me and keeping Walsall in contention for a League One play-off place for 44 games has been a tremendous achievement by everyone concerned.
"Looking to the future, I believe that this decision is in the best interests of both myself and the club."