The execution by lethal injection came after the U.S. Supreme Court denied a petition filed by Franklin's defense team seeking a stay of execution.
Earlier Wednesday, the 8th U.S. Circuit Court of Appeals vacated two stays issued Tuesday by two U.S. district court judges for Franklin, a white supremacist convicted in the 1977 sniper killing at a synagogue, the St. Louis Post-Dispatch reported.
Franklin, 63, was sentenced to die in the state prison in Bonne Terre for killing Gerald Gordon outside a synagogue. Franklin killed at least 18 people between 1977 and 1980, crossing the country and attacking black and Jewish people.
The question of whether the use of pentobarbital constituted cruel and unusual punishment was among issues raised in the request for a stay.
The stay was meant to "ensure that the Defendants' [the state] last act against Franklin is not permanent, irremediable cruel and unusual punishment in violation of the Eighth Amendment," U.S. District Judge Nanette K. Laughrey said in the first stay issued Tuesday.
U.S. District Judge Carol Jackson granted a second stay Tuesday, based on a separate petition challenging Franklin's competency.
The state appealed both stays to the 8th U.S. Circuit Court of Appeals, which ruled early Wednesday Franklin's lawyers did provide enough evidence to warrant a stay of execution
Earlier Tuesday, the Missouri Supreme Court denied Franklin's appeals. Missouri Gov. Jay Nixon denied clemency Monday.
Franklin also admitted to the attempted assassinations of Hustler magazine publisher Larry Flynt in 1978 and civil rights leader Vernon Jordan in 1980, CNN reported. Flynt, paralyzed by Franklin's bullet, had called for clemency for his shooter, saying "the government has no business at all being in the business of killing people."