Despite the spectacular performance, Kwon said the company was in the throes of an "unprecedented crisis" as he announced his intention to step down.
Samsung CEO and Vice Chairman Kwon Oh-hyun said on Friday he'll resign from his post in early 2018, adding another twist in the fallout from the imprisonment of Lee Jae-yong, the de-facto leader of the electronics giant.
He has represented Samsung Electronics at various occasions since the company's heir and vice chairman, Lee Jae-yong, 49, was jailed earlier this year.
Samsung has two other CEOs, each overseeing its mobile phone business and home appliance division.
Samsung Electronics has not yet announced a replacement.
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Kwon's sudden departure may be a calculated legal tactic to seek a softer punishment for Lee, said Shim Jung-Taik, an author of several books on Samsung and its corporate culture.
"It is something I had been thinking long and hard about for quite some time", Kwon said in a statement.
While expressing concern that the company was "confronted with unprecedented crisis inside out", alluding to the conviction of its leader, Kwon said he hopes his resignation can be a good opportunity for the company to turn things around and make bold attempts at innovation.
Friday's personnel announcement came shortly after the company said it was expecting to log 14.5 trillion won ($12.8 billion) in operating profits for the July-September quarter, an all-time record and almost three times the 5.2 trillion won of the same period a year earlier. The boom allowed Samsung to dethrone Intel Corp., the long-time global chip leader, in the second quarter and has yielded record earnings for smaller chip rivals such as SK Hynix.
The company has a league of executives who manage day-to-day operations, but has usually relied on the leadership and the visions of founding family members for direction. Lee Jae-yong's conviction was part of a bribery scandal that reached all the way to the president of South Korea, Park Geun-hye, who was impeached previous year is also serving time in prison. Hearings on his appeal and those of four other convicted Samsung executives began October 12.