If a federal appeals court or the U.S. Supreme Court strikes down Tuesday's ruling, the execution could go forward. Franklin's attorney, Jennifer Herndon, said the execution warrant allows it to be carried out anytime Wednesday.
Herndon said Franklin, who has been diagnosed as mentally ill, didn't seem to fully understand the stay.
"He was happy," she said. "I'm not really convinced that he totally understands that he was going to die."
Franklin, 63, was scheduled to die at 12:01 a.m. (0501 GMT) Wednesday for killing 42-year-old Gerald Gordon in a sniper attack outside a synagogue in 1977. It was one of as many as 20 killings committed by Franklin, who targeted blacks and Jews in a cross-country spree from 1977 to 1980.
He was convicted of seven other murders, but the Missouri case was the only one resulting in a death sentence. Franklin also has admitted to shooting and wounding civil rights leader Vernon Jordan and Hustler magazine publisher Flynt, who has been paralyzed from the waist down since the attack in 1978.
In an interview with the St. Louis Post-Dispatch on Monday, Franklin insisted he no longer hates blacks or Jews.
Like other states, Missouri long had used a three-drug execution method. Drugmakers stopped selling those drugs to prisons and corrections departments, so in 2012 Missouri announced a new one-drug execution protocol using propofol.
But Gov. Jay Nixon ordered the Missouri Department of Corrections to come up with a new drug after an outcry from the medical profession over planned use of the popular anesthetic in an execution. Most propofol is made in Europe, and the European Union had threatened to limit exports of it.
The department turned to pentobarbital made through a compounding pharmacy. Few details have been made public about the compounding pharmacy that makes it because it is part of the execution team, and state law provides for privacy for all associated with executions.
"Throughout this litigation, the details of the execution protocol have been illusive at best," the judge wrote.
Nixon spokesman Scott Holste had no immediate comment about the ruling.