A Brooklyn dad-turned-vigilante went on a frantic search for his runaway daughter — and ended up gunning down an innocent man, wrongly believing he was behind her disappearance, police sources said Tuesday.

The slaying happened May 1, when dad Paul Davis confronted Akeem Booker at Booker’s Canarsie home, believing that his missing 16-year-old daughter was there, sources said.

Davis’ daughter wasn’t at the home at the time — she had been there minutes earlier.

As the father and Booker began arguing, Davis allegedly opened fire, killing Booker and also injuring a second man, Paul Case, according to court papers.

Davis pleaded not guilty Friday in Brooklyn Supreme Court to second-degree murder, attempted murder and other charges. He was held without bail.

The family reported the girl missing April 30, but she returned home on her own days after the murder, sources added.