Stephen Barry McCaffrey, from Trasna Way, Lisnaskea, is accused of damaging or destroying the building by fire on July 22.
A detective constable told the court she believed she could connect McCaffrey with the charge.
A prosecutor said the Public Prosecution Service has decided to proceed with the case on indictment, meaning it proposes to pursue the case against McCaffrey in the Crown Court where trial is by judge and jury.
The charge against McCaffrey refers to the fact that the former workhouse was a Listed Building, because of its importance as part of Northern Ireland's architectural heritage, and belonged to John Trimble. It was opened in 1843 and had been described as one of the finest preserved workhouses in the Province. In more recent years it had been used for industrial purposes, housing a textile factory and window manufacturing business, but was vacant at the time of the fire.
The case against McCaffrey was adjourned until September 26.