Glamorgan are currently sixth in the LV= County Championship Division Two and Hamer issued a joint statement with the county revealing his desire to move into other areas.
"This has been a difficult decision following seven happy years at the club," Hamer said.
"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's chairman Barry O'Brien thanked Hamer for his contribution, with the Welshman's links to the club going back to 2006.
"Alan has indicated to me for a while that he wishes to pursue a number of other opportunities," he said.
"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."
No successor has yet to be found and the club also confirmed Hamer has agreed to continue in his role until the vacancy is filled.
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