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AAP represents 67,000 pediatricians across the country.
The organization has pushed back forcefully against the vaccine recommendations implemented by Health Secretary Robert F. Kennedy Jr., a longtime anti-vaccine activist.
In the lawsuit, AAP says the Department of Health and Human Services retaliated against their organization because of that public criticism.
The millions in canceled grants supported work on sudden infant death prevention, rural health, early detection of birth defects, and more.
The lawsuit was filed in federal district court in Washington, D.C., and says that without court intervention, these programs will end within weeks.
HHS did not respond to NPR's request for comment.