"This is something I've been thinking about for a long time, it's not an easy decision, but I feel it can no longer be postponed," Kwon said in a letter to employees.
"When we are faced with a crisis we have never faced, whether from outside or within the company, I think it's time the company got a new start with new passion and young leaders to face the challenges of the rapidly changing IT industry."
Although Lee does not intervene directly in the day-to-day operations of Samsung Electronics business, Kwon's resignation is proof that this scandal could have a major impact on the operations and culture of the South Korean company.
Currently Samsung's performance is still very good. They announce an approximate financial report indicating that they will benefit greatly.
They estimate their operating profit will triple from last year, showing that they have recovered from the Galaxy Note 7 disaster last year.
Even so, Kwon said, the current performance is thanks to decisions made in the past. He doubts the company's ability to predict trends and grow in the future.
"There's no word to explain how proud I am to have built one of the most valuable companies in the world We have made the long journey to create a company that changes the way people live, work and communicate with each other," Kwon wrote in his letter.
"But, the company now needs a new leader and it's time for me to get into the next round of my journey."
Kwon has been CEO of Samsung Electronics since 2012. He became CEO of Samsung Display in 2016. He joined Samsung in 1985. He led Samsung's semiconductor business before he was appointed CEO. Currently, Samsung has not announced a replacement from Kwon.