"My time at Leicester City provided an insight into the challenges clubs face on a daily basis. The lessons learnt from that experience will not be forgotten," added Clarke, who joined the Leicester City Board in 2000 and helped them through administration in 2002.
Mawhinney, who took the reins in January 2003, was a controversial figure for fans of some clubs - particularly those who suffered points deductions after going into administration, a rule which was brought in for the 2004/05 season.
But the former Conservative Party chairman oversaw a period of change, including the League's rebranding in 2004 - which saw Divisions One, Two and Three replaced by the Championship, League One and League Two.
He also helped introduce the fit and proper persons test for prospective club directors, which was subsequently adopted by the Premier League.
Clarke will spend the next few weeks meeting League and club officials and independent board member Ian Ritchie has backed the League's new chairman.
"Greg will build on the substantial progress made by Lord Mawhinney, focussing on further improving League football's professionalism and business structure, as well as maintaining the momentum on good governance," said Ritchie.
"In short, he will aim to make the league even more effective on behalf of all its clubs."
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