Colin Foy was killed as he sat drinking with his brother
Glen Strong, 27, whose address was given as 4 Royal Irish, the Deanery in Clogher, is accused of shooting 27-year-old Colin Foy in Fivemiletown on Sunday night.
Mr Foy, 27, from Mullaghfad Road in the town was shot while drinking with his brother at the Four Ways Hotel bar in the town.
He had been a regular in the bar where he was shot, just as a disco was about to end at midnight.
Remanded in custody
A detective inspector leading the investigation told Cookstown magistrates court on Tuesday that Mr Strong made no reply when charged.
The officer said he believed he could connect the defendant to the charge.
Mr Strong's solicitor said there had been media speculation that the murder had been sectarian.
The solicitor said to the officer: "Is it true that there is no evidence that my client is or ever has been a member of a paramilitary organisation?"
The detective said to his knowledge this was correct.
The accused was remanded in custody to appear at Omagh magistrates court via a video link on 20 November.
Craigavon murder investigation
Meanwhile, two men aged 47 and 27 are still being questioned about the murder of a teenager in Craigavon in County Armagh early on Monday morning.
Peter Joseph McNally, 19, was asleep in a house on the Westacres Estate in Drumgor when two armed and masked men broke in and shot him at least twice in the head.
Officers believe Mr McNally, who had no fixed address, may have been the victim of a dispute between criminals.
The police have said they do not believe the shooting was sectarian.
It is understood he was on the run from Hydebank Young Offenders' Centre in Belfast.
The police have asked anyone with information about the incident to contact detectives at Lurgan.