The club expects to announce an appointment ahead of the trip to Darlington on Saturday.
Fowler came in during the summer as assistant to Nicky Eaden and took over the reins a little over a fortnight ago, when the former Barnsley man left.
Fowler was in the hot-seat for just two matches, a Buildbase FA Trophy defeat away to Brackley Town and a home defeat against Blyth Spartans in the League.
Chairman Nick Hawkins told the club`s website: “It's a sad day for the club. Lee has been a model professional throughout his time with the Boro. He's a great motivator, a very good coach and has been a pleasure to work with day in, day out. He's a fantastic individual and will be a great asset for whichever club he goes to next.
“On behalf of the club we wish Lee every success in his future, he has a lot to offer and I know he'll bounce back from this. We all know how difficult a task it has been here, and people have seen his effort and application, that he doesn't fold under pressure and that whatever the circumstance, he just knuckles down and gets on with things. In the right conditions he'll thrive, we're very disappointed to be losing him."
Fowler said: "I want to thank Nick for the opportunity that he gave me, I have been humbled by the support of the staff and the fans since I've been at the club. Managers and players come and go but the club is always bigger than any individual and considering how close we came to losing the club, I'm proud to have been part of what was achieved in keeping the Boro afloat.
"I've worked under extremely difficult circumstances and have continually given my all, but, after discussions with Nick, we felt it was best to move forward to try and keep the club in the division with a new appointment".