Saddlers chairman Jeff Bonser said: "He came to the club at a very difficult time. Our playing fortunes were at a low ebb.
"During these past two years, he has led the club to the League Two championship and to a position just outside the League One play-off positions, a very impressive achievement.
"We would like to place on record our appreciation for the work he has undertaken, and to wish him well for the future."
Assistant manager Jimmy Mullen takes temporary charge.
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