Boro finished seventh in the Championship, missing out on a place in the play-offs by one point.
Pulis, who replaced Garry Monk midway through the 2017-2018 campaign, was reportedly due to be out of contract next month and the club will not be extending his deal.
The 61 year-old was regularly criticised by supporters for his style of play, with Middlesbrough scoring just 49 goals in 46 league matches in 2018-2019, but chairman Steve Gibson has thanked the departing manager for stabilising the club.
"Over the past 18 months Tony has been proactive, not only in the ambition to win football matches and promotion to the Premier League, but also in addressing our financial position in order to comply and respect the Championship Fair Play criteria," Gibson told Boro's official website.
"He has ensured that the club is stable and strong for the future. He leaves us in excellent condition."