Stephen Eugene McCourt is accused of murdering Damien Heagney between 30 December 2021 and 6 January 2022.
Mr McCourt, of McGartland Terrace, Dromore, County Tyrone, confirmed he understood the charge during the hearing at Strabane Magistrates’ Court.
No bail application was made and he was remanded into custody.
He is due to appear at Dungannon Court by video link on 2 November.
A murder investigation was launched after the remains of Mr Heagney, 47, were recovered from a reservoir in Cappagh, Co Tyrone, in August.
Mr Heagney, from Cookstown, was last seen in Dromore on New Year’s Eve in 2021.