Stefanovic moved to Fratton Park from Vitesse Arnhem in a £1.85million deal earlier this summer but the 28-year-old has not met the Home Office's criteria for a permit, which require a player to have played in 75% of his country's international matches in the last two years.
Pompey claim this is due to injuries rather than a lack of ability and are to use this as the basis of their appeal.