The company said it will begin a recruitment process to find a new chief executive who will oversee the SSE Hydro, the Clyde Auditorium and Scottish Exhibition & Conference Centre.
Sharkey, who is yet to announce his future plans, joined SEC as finance director in 2002. He was appointed chief executive five years ago.
Sir Ian Grant, chairman of SEC, said: "John has been an excellent business leader for SEC and, as the man who led the team that has brought us the SSE Hydro, has displayed remarkable vision, determination and sheer hard work. He has successfully led the transformation of the business model of the SEC to provide a sharper focus on conferences, exhibitions and ticketing and substantially increased the contributing performance of all three businesses during a challenging construction period.
"His are big shoes to fill and he will leave behind a fantastic legacy to be enjoyed not just by Glaswegians but by music lovers, visitors and conference delegates from across Scotland and beyond."
Sharkey added: "I’m immensely proud of what the SEC team has achieved during my time with the business. Seeing the SSE Hydro from its gestation through construction to its successful opening was immensely satisfying. It is undoubtedly a massive privilege to have had this opportunity and now it’s time for me to take on another challenge."
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