Kennedy, an environmental lawyer and anti-vaccine activist, has repeatedly shared debunked theories about vaccines.
Facebook, which owns Instagram, announced Monday that it would flag or remove posts from users and groups that spread misinformation about vaccines.
The company said it's working with the World Health Organization to stop the spread of debunked claims.
Kennedy, the son of former Sen. Robert Kennedy and nephew of President John F. Kennedy, had more than 800,000 followers on his Instagram page when his account was removed. His accounts on Facebook and Twitter, which shared much of the same content, were still active early Thursday.
"We removed this [Instagram] account for repeatedly sharing debunked claims about the coronavirus or vaccines," a Facebook spokesperson told Variety.
The company said, however, Kennedy's Facebook account will not be shut down.
Kennedy has been identified as "one of the most influential online anti-vaxxers" by the nonprofit Center for Countering Digital Hate. He often posts articles from the magazine of the organization he founded, Children's Health Defense, an anti-vaccine charity.
In a January post, Kennedy spread a theory that baseball legend Hank Aaron died of COVID-19 after being vaccinated. The Fulton County, Ga., medical examiner refuted those claims and said Aaron died of natural causes at the age of 86 on Jan. 22.
Anti-vaccine groups have flourished on social media, even before the pandemic, and about 31 million people followed related pages on Facebook in 2019, according to a study in The Lancet.