The announcement comes as the South Korean company grapples with an unprecedented smartphone recall that has wiped out billions of dollars from its market value. It recalled 2.5 million Galaxy Note 7 smartphones earlier this month and urged consumers around the world to stop using the phone immediately as airlines and aviation regulators urged the same due to safety concerns.
In announcing Lee's nomination to the board, the company said in a statement that the Samsung board believes that "the time is now right."
The nomination signals a new era for Samsung under a third generation of its founding family.
Lee, 48, a Harvard-educated vice chairman at Samsung, is thought to have been making key decisions for Samsung since his father Lee Kun-hee, 74, has been hospitalized after suffering a heart attack in 2014, leaving him unable to oversee the company.
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Samsung officials have said given the Confucian tradition of filial piety, it has been difficult for the younger Lee to take on a bigger leadership role while his father is still alive.
Lee's nomination will be put to a shareholder vote on October 27.
Shareholders will also vote during the October meeting on Samsung's decision to sell its printer business to HP Inc.
Palo Alto, California-based HP has said it agreed to buy Samsung's printer business for USD 1.05 billion. Samsung's printer business has 6,000 employees and a production base in China.
Samsung has been working to streamline and restructure businesses that are not crucial for its future.