Root, 35, England's all-time leading run scorer in tests, captained the side in a record 64 matches between 2017 and 2022, winning 27 of them.
He returns to the role after Stokes retired from international cricket in June and will lead England in the three-test home series against Pakistan starting on August 19th.
"It is a great honour and privilege to be asked to be England men's test captain again," Root said in a statement.
"The test captaincy is a difficult but hugely rewarding job and, after enjoying a brief taste of it again working with Brendon McCullum last month, I am excited to lead this next generation of players forward."
"The opportunity to do that alongside Stephen is also a huge motivator. He has proved over a long period of time that he is an exceptional leader with a great knowledge of the game, and I am looking forward to working with him and helping to build a winning environment."
Root led England in the second test against New Zealand at The Oval this summer in Stokes' absence.
Fleming, 53, takes charge of an England side looking to rebuild after a decline in results and a series of off-field incidents that led to McCullum's dismissal. New Zealander McCullum remains coach of England's white-ball teams.
"I'm incredibly excited to be joining England as Test Coach. It's one of the most prestigious coaching positions in world cricket and I am honoured to be appointed," Fleming said in a statement.
"I'm particularly looking forward to working with Joe Root as captain - a generational talent who has achieved so much already.
"There is still plenty more to come from him, and I’m excited to support him so he can enjoy and thrive in the role in what is a different context to his first stint."
Fleming, who played 111 tests for New Zealand and captained the team, will assume the role of coach after the test series against Pakistan, with assistant coach Marcus Trescothick leading the side on an interim basis until then.
