In an announcement the Mirror said Kelly "has played a pivotal role in transforming both the newspaper and digital platforms", having been the lead on the Mirror website and newspaper redesign in 2008 and was also involved in its latest site redesign earlier this year. He also helped launch MirrorFootball.co.uk and 3am.co.uk in 2009.
Last week the publisher announced that following the relaunch earlier this year and the company's "investment in digital resource" digital revenues had grown by 12.5 per cent in the first half of 2012.
Its nationals division, including the Daily Mirror, Sunday Mirror and the People, was also said in the interim report to have "performed strongly in the period with operating profit increasing by 11.8 per cent". Overall the company reported a rise of more than 20 per cent in pre-tax profit.
In today's announcement Kelly was quoted as saying that he has "had the most blessed 18 years and the privilege of working with an extraordinarily talented team".
"I am incredibly proud of everything that we have achieved together.
"But I have a couple of very exciting new opportunities ahead of me and I know the Mirror is in terrific hands. It feels like the perfect time to move on."
The announcement stated that Steve Anglesey, deputy publishing director, will take on Kelly's role when he leaves at the end of the month "until a full-time replacement is found".