Hamer was appointed to the role in 2009, but has been with the Welsh county since joining as finance and commercial director in 2006.
He will remain in charge for the rest of the season and Glamorgan say they will announce his successor shortly.
"This has been a difficult decision following seven happy years at the club," said Hamer.
"I am, however, convinced that this is the right time for me to build on my successes at the club and to take on a new challenge."
Glamorgan cricket chairman Barry O'Brien paid tribute to the work Hamer had done at the Swalec Stadium.
"Alan has indicated to me for a while that he wishes to pursue a number of other opportunities," said O'Brien.
"As our previous finance and commercial director and chief executive since 2009, Alan has made a major contribution to the club including managing the successful 2009 Ashes and this year's ICC Champions Trophy which helped put Glamorgan Cricket and the Swalec Stadium on the world cricket map.
"I am very grateful to Alan and respect his decision to seek a new challenge.
"I am also pleased that Alan has accepted the committee's invitation to become an honorary life member in recognition of his contribution to the club."
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