The England and Wales Cricket Board said Tuesday that the former Zimbabwe wicketkeeper-batsman had committed himself to a renewed permanent deal.
It did not say how long Flower had signed for.
"Andy Flower has made a huge impact during his time as England team director and I am delighted that he has committed to the role," England managing director Hugh Morris said. "Andy's outstanding leadership, commitment, and his open and honest approach have been key factors in the success the England squad has enjoyed over the last two years.
"I have no doubt that under his direction we will continue to see England improve as we strive to become the No. 1 side in the world in all formats of the game."
The 43-year-old Flower was promoted from assistant coach to take charge of England at short notice in 2009 when Peter Moores was fired following a dispute with Kevin Pietersen, who also lost his job as captain.
After a dismal tour of the Caribbean, he rallied the side to a 2-1 home series win over Australia, regaining the Ashes that had been lost 5-0 two years earlier.
England won the World Twenty20 title in May 2010 and then won the Ashes in Australia for the first time since 1986-87, continuing a rise from sixth in the test rankings when Flower arrived to third behind India and South Africa.
"I am very pleased with the advances we have made as a squad over the last two years in all formats of the game," Flower said. "Regaining the Ashes in 2009 and retaining them last winter and the 2010 World Twenty20 title are obvious highlights, but there is still plenty more we want to achieve in the longer term."
Although England has climbed a place to fifth in the one-day rankings in the same period, its one-day form remains patchy. It only just reached the World Cup quarterfinals this year after embarrassing losses to Ireland and Bangladesh.
"We have made no secret of our determination to become the No. 1 side in the world and challenge for global titles and I feel we have been making steady progress," Flower said. "I firmly believe we have the talent amongst the playing squad and management team to help us realize our ambitions and am looking forward to testing ourselves against quality opposition this summer and beyond."
England hosts Sri Lanka and India over the next five months.