The charge is the latest in a series of legal follow-ups to the attack by the Real IRA, which is regarded as one of the worst bombings of the Northern Ireland troubles.
The man, who is aged 34 and from Co Louth in the Irish Republic, was arrested on Monday. He is due to appear before magistrates in Enniskillen, Co Fermanagh, this morning.
The charge against him states that between 11 and 16 August 1998 he supplied the maroon Vauxhall Cavalier car which exploded in Omagh, killing men, women and children, including a woman who was carrying unborn twins.
Last month Colm Murphy, the only man to be convicted in connection with the bombing, had his appeal overturned by a Dublin court. He is to face a re-trial. Another man is already facing a charge of possessing the timer used to set off the car bomb.
Relatives of some of those killed are pursuing damages against five republicans, believed to be associated with the Real IRA, in a civil action due to come to court in Belfast in the next few months.
Earlier this week the relatives said they were disappointed when a Dublin court said it had no jurisdiction to grant their application for materials used in the prosecution of some of the five.
The relatives had asked for trial transcripts and statements used during the trials.Reuse content