The House voted 79-15 and the Senate voted 32-6 to override, The Louisville Courier-Journal reported Wednesday.
The bill states a person's sincerely held beliefs cannot be infringed on unless the government can show "clear and convincing evidence" why it must do so.
In a statement after the vote, Gov. Steve Beshear repeated his veto message that he had "significant concerns" the bill would cause "unintentional consequences that could threaten public safety, healthcare and individuals' civil rights."
He expressed additional concerns about the possible cost of the law to local governments, the impeding of economic development efforts, the possible withholding of medical care and the use of religious beliefs to justify abuse.
Human rights groups said the bill could be used to invalidate local laws that protect gays and lesbians from discrimination.
Martin Cothran, spokesman for the Family Foundation, said the wide vote margin should send a message to Beshear and opponents of the bill "that this kind of deception is not appreciated by the majority of the state's elected lawmakers."