McFadden made his senior championship debut for Donegal in 2002. That year, Donegal drew against Dublin by a scoreline of 0–14 to 2–8 in the All-Ireland Senior Football Championship quarter-final held on August Bank Holiday Monday, Dublin eventually winning the replay. He started the first game of Brian McEniff's last spell as Donegal manager, a league defeat to Galway in Tuam in February 2003, during which he scored two points. In the 2003 Championship, Donegal defeated Galway, the All-Ireland champions of two years previous, in the All-Ireland quarter-final replay at McHale Park in Castlebar. That victory qualified them for a semi-final against reigning All-Ireland Senior Football Champions Armagh, whom Donegal led with 14 men (after Raymond Sweeney was harshly sent off for a second yellow card) until a last minute penalty from Oisín McConville led to Donegal losing the game by a scoreline of 2–10 to 1–9. McFadden made a late substitute appearance for Brendan Devenney in that 2003 All-Ireland Senior Football Championship semi-final against Armagh. A pivotal game in McFadden's development occurred in the 2004 Championship, when McFadden scored 1–7 against Tyrone in Donegal's Ulster semi-final victory. Tyrone were the reigning All-Ireland champions and the "Irish Examiner" reported: "The new golden boy of Gaelic football, Colm McFadden, torpedoed the All-Ireland champions with a magical display of finishing". But Donegal did not do so well against Armagh in the final at Croke Park. And so ended the high points of McFadden's early inter-county career. He missed the 2006 Championship due to his studies in Liverpool, and a perceived lack of fitness on his part.