Flower has been working with the Lions for the last five-and-a-half years. The Zimbabwean was an assistant coach with the senior England team in 2007, before taking up the role of head coach in 2009.
The 51-year-old led England to No 1 in the Test rankings in 2011, but pointed to the 3-1 Ashes series win over Australia prior to it as one of his many highlights during his tenure.
“The Ashes victory in 2010-11 stands out,” he said.
“It’s difficult to win in Australia and to do it so comprehensively was a really proud moment in my coaching career. It was wonderful to watch those young men take on that challenge successfully and have a great time doing it.
“The win in India in 2012-13 was a highlight too, to overcome some great players in tough spinning conditions was a special victory.
“So was the T20 World Cup win in 2010. The way we played our cricket, with such freedom and aggression, really was fun to be part of.”
Flower said he was grateful for the support he received while in charge of England and proud to have played an important role in the development of some of the country’s top cricketers.
“I’d like to thank the captains I worked with longest, Alastair Cook and Andrew Strauss, for their commitment and friendship over the years,” he added.
“It’s been a privilege to work with all the players. Sometimes, in high-pressure environments, as a coach and a mentor you hold a very responsible position.
“You end up sharing some really intimate moments – over a beer in the dressing room, working hard together in the nets, or listening to a personal problem and helping them work through that – and it’s a privilege to be able to contribute and influence these young guys’ lives.”
Ashley Giles, managing director, England men’s cricket, added: “Andy moves on with every best wish from all of us at ECB for his outstanding contribution to the English game over the last 12 years.
“It has been a pleasure working with Andy, who sets such high standards of professionalism and preparation for the teams he leads. I have no doubt he will enjoy further success in the years to come.”