Bower guided the club to back-to-back play-off seasons in the National League North.
But the time has come for a new challenge - and he leaves with fond memories of his time in Yorkshire.
The club are expected to name his replacement soon with fans told to stand by for a big announcement on Tuesday night.
“I have thoroughly enjoyed my time at Bradford (Park Avenue) over the past three seasons and I’m proud of what we have achieved together as a club in that time,” Bower told the club’s website.
“I would like to thank everybody who has contributed to our success, in particular Gareth Roberts as, without his support, the incredible moments and memories we have from the past three years, would not have been possible.
“I wish everyone at Bradford (Park Avenue) the best of luck for the new season and beyond.”
Bower’s assistant-manager Danny Boshell also left the club.