Whelan, who will be 33 in October, made his championship debut with Dublin in the Leinster final in 1996 and became a central figure in the side winning six Leinster championship medals.
He served two years as Dublin captain in 2003 and 2004.
Under the new Dublin management, the Raheny club man was used as a substitute during this year's championship and has now decided, due to personal commitments, that he is to call time on his county career.
"My body isn't recovering as quick as I'd like," said Whelan. "Every year the commitments are getting bigger. I reached a stage in my own head where I was quite clear that it was time to move on. But I've enjoyed every minute of it. For 14 years it's been a childhood dream come true. I wouldn't change any bit of it," he added.