Roger Thorson had appealed to the 5th U.S. Circuit Court of Appeals after a Mississippi federal judge dismissed his lawsuit against Corrections Commissioner Christopher Epps.
On Wednesday, a three-judge rejected Thorson's claim.
The panel said most of Thorson's claims about the protocol were speculation.
"Mississippi has chosen, by both method of execution and the procedure for administration of the lethal injections, to alleviate cruelty and reduce 'harm' in capital punishment," wrote Judge Edith H. Jones.
Thorson was sentenced to death for killing a former girlfriend on the Mississippi Gulf Coast in 1987.
Thorson's case marked the second time the 5th Circuit has considered a challenge to Mississippi's lethal injection protocol.
In 2008, the 5th Circuit ruled Mississippi's method "appears to be substantially similar" to a protocol affirmed by the U.S. Supreme Court. The challenge was brought by Leo Dale Bishop, who later was executed for his role in a 2000 slaying.
The language was significant because the U.S. Supreme Court ruled in April 2008 that Kentucky's method is acceptable, as are "substantially similar" protocols. That ruling came after two death row inmates in Kentucky challenged the procedure in a lawsuit that blocked executions around the country for months.
That defense was raised by the state of Mississippi in response to Thorson's lawsuit. The state said all the issues raised by Thorson were settled with the U.S. Supreme Court and the 5th Circuit follow-up in the Bishop case.
But Thorson, in court documents, said there were significant differences between how executions are conducted in Mississippi and Kentucky.
Thorson contended that "much of lethal injection protocol in Mississippi is based on pattern and practice and not written regulations that govern all corrections officials in Mississippi."
The 5th Circuit panel said Wednesday that Mississippi's written instructions detail virtually every step related to an execution.
"Those steps not written are systematically ensured by conscientious training, repeated practice runs, and the experience of the participants relied on by the prison," Jones wrote for the panel.