Lee was appointed in September following the departure of Justin Merritt.
Lee said: "After this season with Witney Town I regret that I have made the decision to resign as manager.
“My time with the club has been memorable and I thank each individual player for their commitment and honesty. In addition the team's coaching staff who devoted time and professionalism to the club.
“My decision has not been an easy one. However, circumstances at the club have proven influential in prohibiting with I feel a successful football club requires as a sound foundation for both players and staff.
“I would like to personally thank Andy Lyne for support and encouragement and wish all at Witney Town every success in the future."