The former England manager confirmed he had departed by mutual consent after a dismal run of form saw them fall out of contention for the Eredivisie title.
McClaren made himself a hero at Twente by winning the club's first domestic title in 2010, before leaving for German side Wolfsburg.
He returned in January 2012 after being sacked by Nottingham Forest.
Twente topped the Dutch table at Christmas, sparking hopes of another glorious season.
But the club are yet to win in 2013, and Saturday's 2-1 defeat at Heerenveen left them in fifth place, six points behind leaders PSV.
McClaren said in a statement: "After the defeat to Heerenveen on Saturday, I met the President on Sunday. We tried to find a solution to the difficult period the team has endured over the last four weeks.
"We discussed the expectations of the club, how European qualification was key each season and finishing in the top four. Despite being joint top at the winter break and even second four weeks ago, recent results and performances have seen major criticism, protest and demonstration from the supporters and the media.
"We talked about how we could change the situation and relieve the pressure on the team which has clearly affected its performance. Unfortunately, Saturday's result has seen further adverse reactions and with two home games coming up, we feel the team needs the support and backing from the supporters.
"I also needed assurances about my position now and in the future, which I appreciate in the present situation is difficult. After much discussion and deliberation, those assurances weren't forthcoming and we have agreed it's in the best interest of the club going forward that I leave.
"The club is bigger than any one individual and Twente is too big in my heart to stand in the way of its progress! I leave with the team with 10 games to go, still able to achieve its expectations of a top-four finish, which I am positive they will do.
"I leave a proud man to have managed Twente. It has brought me many good memories and one of the greatest days in my career when winning the title in 2010. The support received from the club, staff, players and fans has always been much appreciated and I leave sad and disappointed it has ended in these circumstances, but wish the staff and the team success in the future."
The club have only 10 league games remaining to halt the slump and secure a top-four finish.
"We thought that the disappointing results under McClaren could be turned around," chairman Joop Munsterman said. "Steve, however, made clear that in the best interest of the team it would be better that he stepped down. We understand his decision and respect it."
FC TWENTE EREDIVISIE RESULTS 2013
19/01 - Twente 0-0 RKC Waalwijk
27/01 - Feyenoord 0-0 Twente
03/02 - Twente 2-4 Utrecht
10/02 - PEC Zwolle 1-1 Twente
16/02 - Twente 1-1 Willem II
23/02 - Heerenveen 2-1 Twente
