He is widely expected to be replaced on a temporary basis by England academy director Peter Moores although the ECB declined to confirm this in a news conference.
A spokesman said a replacement would be named within 48 hours.
"The likelihood is that the person who will be appointed will come in on a temporary basis but I don't rule out the possibility that we could, before the start of the West Indies series (starting in May), have confirmed a permanent appointment," ECB chairman David Morgan told reporters.
Fletcher, who has held the post since 1999, had come under pressure after England were knocked out of the World Cup in the second round following another poor display in the nine-wicket defeat by South Africa on Tuesday.
England's disappointing tournament follows a 5-0 mauling by Australia in the Ashes Test series and the 58-year-old Zimbabwean was left with little choice but to resign.
ECB chief executive David Collier said in a statement: "ECB would like to formally put on record our grateful thanks to Duncan Fletcher for his outstanding service to cricket throughout England and Wales.
"He can be justifiably proud of a record which includes an Ashes Series victory over Australia, a record eight successive Test wins and Test series wins abroad in Pakistan, Sri Lanka, West Indies and South Africa as well as the Commonwealth Bank series success in Australia.
"England's rise to number two in the ICC Test Championship is in no small measure due to his rigorous planning and excellent coaching skills.
Fletcher said he now sought new challenges. "I always said that I would review my position as England coach nearer to the end of this winter," he said in the ECB statement.
"Earlier in the World Cup I came to a decision about my future and I discussed stepping down as head coach with the ECB prior to England's game against Bangladesh.
"I feel it is in the team's best interests over the long term that I should move on and seek a new challenge elsewhere.
"This has been a difficult winter for the team and for me personally but I believe that my record as coach over the past eight years is one in which I can take great pride."
Bangladesh are the sole Test team England have managed to beat so far in the tournament and even that victory was a nervy four-wicket win. Their only other wins came against outsiders Canada, Kenya and Ireland.
Their group stage qualification was marred by a late night drinking scandal which led to Andrew Flintoff being stripped of the vice-captaincy and banned for one game.
Several players and two coaches were also fined for the incident in St Lucia following their opening defeat by New Zealand.
Until the Ashes whitewash at the turn of the year, Fletcher's Test record had been excellent, driving England to second in the Test rankings, even if the team's one-day performances have always been patchy under his guidance.
Fletcher's finest moment came in 2005 when England beat old enemy Australia 2-1 at home to win the urn for the first time since 1987.
The famous victory followed Test series wins in West Indies and South Africa and a run of seven home Test victories in a row in 2004 against New Zealand and West Indies.