John Clark, 22, is alleged to have attacked and killed the fellow inmate at Barlinne Prison in Glasgow during the early hours of Thursday.
He made no plea or declaration during a brief appearance at court yesterday and was remanded in custody until March 28.
His alleged victim was a 22-year-old sex offender.
Detectives were called out to the scene after the prisoner was found in his cell in E Hall on the fourth floor of the jail.
Clark, whose address was listed as Barlinnie Prison, was arrested and detained in police custody overnight before being brought to court yesterday.
The Scottish Prison Service confirmed that there had been a death at the jail but it refused to comment further.
A report has been submitted to the procurator fiscal.