He has at times supported abortion rights and at times voted to limit access to abortion. He opposed federal funding of Planned Parenthood, and opposed sanctuary cities, gun control, gay marriage, and federal regulation of greenhouse gas emissions. He endorsed Donald Trump in the 2016 presidential election. He voted to repeal the Patient Protection and Affordable Care Act (Obamacare) and replace it with the American Health Care Act (AHCA). Frelinghuysen was criticized for using a fundraising letter to "a member of an activist group opposing him to her employer" which resulted in a complaint by the Campaign for Accountability made with the Office of Congressional Ethics.