The 51-year-old will take up the post on October 1 this year.
He was nominated by the current President Roger Knight at MCC's Annual General Meeting, which took place yesterday at Lord's here.
Currently the Chairman of Cricket, having been elected in October 2013, Fleming will be the youngest MCC president in 36 years, since Peter May served in 1980.
"I would like to thank Roger Knight for nominating me to succeed him as MCC President. I am very honoured and very humbled to be asked to follow in the footsteps of some of the most extraordinary people ever involved in the game," Fleming, who played 11 ODIs for England in the late 1990s, said.
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"Cricket around the world faces unique challenges and opportunities, and MCC has a vital part to play at a local, national and international level. I have always believed that MCC's role within cricket is to support where necessary and lead where required, and working alongside Derek Brewer and the team I look forward to combining my role as Chairman of MCC Cricket with the Presidency of this great club.
Since the MCC Foundation first committed financial support to Afghan Connection in 2009, 52 pitches have been built in 22 Afghan provinces, with over 100,000 local children attending cricket training as a result.