After discussions with the club over their league position and cup exits, the 55-year-old handed in in his resignation, which was accepted by the club.
Assistant manager Russ Penn has taken over on an interim basis for 'the next three or four matches.'
A statement from the club said: "Discussions were held with John earlier this week in light of the team’s current league position and early exit from the FA Cup and FA Trophy.
"While managing the club has had its challenges this season, we feel strongly that with the players at our disposal and with what is a considerable budget for this division, we should be in a far better situation than we currently find ourselves.
"At the end of these discussions, John offered his resignation which was accepted by the club.
"We would like to thank John for his effort while in post and wish him well for the future.
"The club feels it is still well placed to achieve this season, and as such, the owners will take their time in appointing the team’s next manager – an appointment which will be crucial.
"In the interim, assistant manager Russ Penn will take charge of the team for at least the next three or four matches, with our full support.
"It is clear that Russ is extremely popular with both players, staff and supporters and we are confident they will respond accordingly during a busy period of fixtures.
"We’d urge all Harriers fans to give Russ their full support, starting with this weekend’s game with Southport at Aggborough Stadium."
Harriers currently sit 17th in the National League North with five wins from 16 games.