Jones, the longest serving member of the board, announced his resignation at the board's regular meeting on Monday.
"It is time for me to pursue other interests," said Jones.
"The 26 years I have spent on this Board serving the students of the Boise School District have been some of the most rewarding of my life. When I was first elected I never imagined I would serve nearly three decades. I am proud of what we have accomplished for students during that time."
Board President A.J. Balukoff called Jones an outstanding member of the board who "contributed significantly and positively to make the Boise School District what it is today."
During Jones' time on the board, the district received numerous state and national recognitions for improving student academic performance and providing exemplary programs for students. Voters approved facility bond elections and supported a 2012 levy effort to maintain class size. The district also increased its school choice program offerings and added Advanced Placement coursework.
The district will announce plans for the selection of Jones' replacement at a later date.
Jones served as president of the board from 2000 to 2008.