The US celebrity, who has been on the firm's board since 2015, said she would not stand for re-election at its next shareholder meeting in May.
Ms Winfrey recently revealed that she used weight-loss drugs as a "maintenance tool."
Shares in Weight Watchers International fell by 27% in extended New York trade.
Ms Winfrey said in a statement that she would continue to work with Weight Watchers "in elevating the conversation around recognizing obesity as a chronic condition."
The influential talk show host and businesswoman also said she will donate all her shares in the firm to the National Museum of African American History and Culture.
Ms Winfrey is one of the biggest shareholders in Weight Watchers with a stake of around 10%.
When Ms Winfrey started working with the company almost a decade ago, she joined the Weight Watchers programme and shared her experiences with other members. She had previously spoken publicly about her battles with weight.
Her decision to leave the board comes as the company contends with a major shift in the weight-loss industry after the launch of anti-obesity drugs such as Wegovy and Saxenda.
Also on Tuesday, Weight Watchers published its latest financial figures, which showed a net loss of $88.1m (£69.6m) for the last three months of 2023, more than twice as much as the same period the previous year.
In March 2023, the company announced it would buy digital health company Sequence "as a natural step" given "the advancements in chronic weight management medications."
Sequence describes itself as a weight loss programme, which offers a suite of services to its subscribers. As well as advice from fitness coaches and dietitians, it is also able to prescribe drugs such as Ozempic and Wegovy.
Weight Watchers boss Sima Sistani said the $132m deal would allow members to benefit from both its approach to "nutrition and behaviour-change" as well as prescription medications.
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