The 45-year-old said that he rejected a new deal with the club because he felt it was time for "careful personal consideration" about where his career is heading.
"In light of the continuing speculation over my role as Manager of Exeter City Football Club, I feel it is appropriate to announce that I have rejected the new and improved contract offered to me," Exeter's official website quotes Tisdale as saying.
"I would like to note that the club did everything in its power to keep me and for that I am extremely grateful. However, I feel now is the correct time for some careful personal consideration regarding my own career.
"To do so, I must first provide the club with absolute certainty in its planning for the upcoming campaign by standing aside."
Tisdale has spent the last 12 years at the Grecians, making him the longest-serving boss in the Football League before he quit.