The 18-year-old Londonderry-born player has informed manager Nigel Worthington he wants to play for the Republic of Ireland instead.
Duffy has withdrawn from the squad to face Albania in a friendly in Tirana on March 3 after being named in the party today.
Absent: Captain Aaron Hughes (right) is not named in the squad
He looked set to win his first cap in the absence of captain Aaron Hughes and his defensive team-mate Chris Baird.
However, Duffy, who has made two appearances for Everton in the Europa League this season, sees his future with the Republic like Manchester United's Darron Gibson.
Northern Ireland squad to face Albania in Tirana on March 3Taylor (Birmingham), Tuffey (Partick), CarsonSunderland); McAuley(Ipswich), Evans (Man Utd), Craigan (Motherwell), McCartney(Sunderland), McGivern (Man City), McGinn (Celtic), McCann (Scunthorpe), O'Connor (Scunthorpe), Davis (Rangers), Brunt (WestBrom), Shiels (Doncaster), Johnson (Plymouth), Clingan (Coventry);Healy (Sunderland), Feeney (Cardiff), Lafferty (Rangers), Little(Rangers), Kirk (Dunfermline), Patterson (Coleraine).
Worthington is believed to be disappointed at Duffy's change of heart.He has come through the system with the province and was captain of theUnder 19s before graduating to the Under 21s.
Duffy was one of three uncapped players called up along with Coleraine striker Rory Patterson and Sunderland goalkeeper Trevor Carson.
Patterson, who is joining Glentoran next season after signing a pre-contract agreement, has scored 31 goals this term.
Carson is one of three goalkeepers in the party and joins veteran Maik Taylor and Jonny Tuffey.
Worthington has named Jonny Evans even though Manchester United are playing Aston Villa in the Carling Cup final on Sunday at Wembley.
No Scotland recall for Rangers goalkeeper Allan McGregor after injury in alleged late-night Glasgow attackWigan whizzkid McCarthy handed first Republic of Ireland call up by TrapattoniTHE LIST: Top 50 English players who should be on Fabio Capello's radar