"It is something I had been thinking long and hard about for quite some time", Kwon said in a Samsung announcement.
The abrupt departure of Kwon, who had been acting head of the tech conglomerate since its de facto leader, Lee Jae-yong, was detained for a bribery trial, throws Samsung into yet another leadership vacuum.
Lee - who took the reins of the company after his father's heart attack in 2014 - was found guilty of bribing a friend of former South Korea President Park Geun-hye to secure a merger that would tighten his grip on Samsung. While Samsung was battered a year ago following the Galaxy Note 7 debacle, it seems to have bounced back and will soon announce a much rosier financial position.
"Fortunately, the company is now producing best-ever results but this is merely a fruit of decisions and investment made in the past", he said in a statement.
"[Samsung] has been showing record performances", Kwon said.
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However, in a sign of good news for the company, its estimated operating profits for the third quarter of 14.5 trillion won (US$12.8 billion) marked a record for quarterly profit, almost tripling the 5.2 trillion won earned a year earlier.
Kwon added the company is facing a grave situation despite it making record-breaking earnings.
"Kwon himself might have thought over the issue for a long time", a Samsung spokesperson said, "but the notice itself was a surprise internally as well".
Samsung said its July-September profit was likely 14.5 trillion won ($12.81 billion), compared with an average forecast of 14.3 trillion won from a Thomson Reuters survey of 20 analysts.
Kwon joined the company in 1985 as a researcher of the company's Semiconductor Research Institute in the United States.
Amazingly, Kwon's move was announced almost simultaneously with Samsung's third-quarter guidance, which predicted a record operating profit due largely to its business of producing chips and other components for mobile devices-a division that Kwon helped build. Semiconductors accounted for $7.2 billion during the quarter, Reuters reported, marking the company's top-performing business.