The Trinity-Spadina trustee said in a letter Friday he would leave his post by 5 p.m. He had previously announced this term would be his last, but there were still months left his four-year mandate.
Donna Quan, the director of education at the school board, said in a statement it was a pleasure working with Bolton.
"He has been a champion of alternative, international and continuing education," she said.
There has been turmoil at the school board recently, which saw Bolton call in off-duty police officers to watch over TDSB meetings after some trustees complained of harassment and other bad behaviour.
Several recent audits of the school board revealed both irregularities in spending, and trustees who had ties to charitable groups that received funding from the TDSB.