Scots-born McCafferty, 70, from Raby Street off the Ormeau Road in south Belfast, was accused at Belfast Magistrates’ Court of carrying out the offence which is alleged to have taken place between 2011 and 2014.
At the time, the victim was aged 13-16.
McCafferty was remanded in custody until next month.
The pensioner worked for several football clubs during the 1980s and 90s as a scout, kitman and youth coach.
The clubs included Celtic, Hibernians and Falkirk.
He moved to Northern Ireland seven years ago after mysteriously quitting Scottish football.