But in his resignation letter Kwon explained that because Samsung is facing "unprecedented crisis inside out", the time has come for the company to "start anew, with a new spirit and young leadership".
His decision to resign comes at a time when the company tries to clean up its reputation amidst bribery case.
In an emotional letter sent to all employees, Kwon said that while announcing his retirement was the most hard thing for him to do, he believed it was the right time and in the best interest of the company, amid continuing controversy around Samsung vice-chairman Lee Jae-yong, arrested on charges of bribery. He will serve till his term as Samsung Electronics' chairman of the board ends in March 2018. "It has not been an easy decision, but I feel I can no longer put it off".
The "unprecedented crisis" that Kwon may be alluding to is the arrest of Lee Jae-yong, the de facto leader of the Samsung. Kwon, who turns 65 on Sunday, plans to stick around for six months until a successor, most likely from inside the company, is installed. Operating income nearly tripling to a record 14.5 trillion won ($12.8 billion) in the three months ended September, according to preliminary results.
The boost was driven by strong sales from Samsung's semiconductor business, which supplies memory chips for rival phone makers like Apple.
He played a major role in strengthening Samsung Electronics' position in the memory chips business across the world.
Yonhap Infomax data, based on research from 21 securities firms, also showed that Samsung is expected to post an operating profit of 16 trillion won in the fourth quarter, up 74 percent from a year earlier.
Kwon joined Samsung in 1985 as a researcher in the company's Semiconductor Research Institute in the United States.
"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 CEO Kwon Oh-hyun has announced his resignation from the company.