District Judge Kristine Baker's order came hours after Arkansas Governor Asa Hutchinson dismissed calls for an in-depth review.
Kenneth Williams, the fourth prisoner executed in eight days, convulsed and groaned, witnesses said.
His lawyers described his death on Thursday as "horrifying".
In addition to the examination, Judge Baker also ordered the preservation of blood and tissue samples from Williams's body.
Her decision came after Jason McGhee, a death-row inmate who had also been scheduled to die on Thursday, filed an emergency order.
He and three others who had been scheduled to die before the state's supply of sedative - part of the lethal injection used to execute prisoners - runs out have all won reprieves.
Earlier, Governor Hutchinson had rejected calls for anything more than a "routine" check into the execution, while Senator Trent Garner - who witnessed the execution - said Williams did not "seem in pain".
But Shawn Nolan, who represented Williams, filed a motion which argued that if "the [drug] midazolam fails to keep the prisoner under anaesthesia, the prisoner would be awake and aware but unable to move or speak or even open his eyes, so he would then look completely serene despite being in agony".
Williams was initially spared the death penalty when he was sentenced to life in prison for the 1998 murder of 19-year-old cheerleader Dominique Hurd.
After a month in the penitentiary, he escaped in October 1999 by hiding in a barrel used to carry kitchen refuse.
Not far from the prison, he encountered Cecil Boren, 57, on his farm.
He killed Mr Boren, shooting him multiple times, and stole his Ford F-150 pick-up truck.
Williams drove north to Missouri, where he led police on a chase that caused the high-speed death of 24-year-old delivery driver Michael Greenwood.
After being jailed, Williams became an ordained Protestant minister, and wrote his autobiography as well as a book warning against gang life.
|Kenneth Williams's lawyers said he was intellectually disabled. GETTY IMAGES|
Judge orders Arkansas to conduct autopsy on executed inmate
Washington (AFP) - A federal judge has ordered the Arkansas authorities to conduct an autopsy on the body of an executed inmate whose lawyer described his death as "horrifying," including jerking and convulsions during his lethal injection.
Judge Kristine Baker of the US Court for the Eastern District of Arkansas issued the order late Friday, less than 24 hours after the state executed the 38-year-old convicted multiple murderer Kenneth Williams.
He was the last of four inmates put to death in a week -- the first executions by the conservative southern state since 2005.
Arkansas officials had said the compressed timeline was necessary because the state's stock of a sedative used in the lethal injection, midazolam, was set to expire at the end of April.
In addition to the autopsy, the judge also ordered the Arkansas authorities to preserve blood and tissue samples from Williams's body.
The emergency motion "for preservation of evidence" was filed by Jason McGehee, a death-row inmate who had been scheduled for execution on Thursday.
He and three other prisoners who were also set to die over an 11-day period before the end of this month have won reprieves.
Williams's lawyer Shawn Nolan has said the condemned man suffered during his execution.
"Within three minutes into the execution, our client began coughing, convulsing, jerking and lurching," he said.
Nolan and the American Civil Liberties Union have called for an investigation into whether the execution on Thursday night amounted to death through torture.
He dismissed as a "whitewash" a comment by Arkansas Governor Asa Hutchinson's spokesman that the physical agitation was an "involuntary muscular reaction" caused by one of the drugs.
Many of the legal clashes over the string of executions focused on midazolam, which is meant to render condemned people unconscious before other drugs cause death.
Critics say it does not always adequately sedate prisoners, potentially causing undue suffering.