After losing two finals in a row to Bellaghy in 1999 and 2000, Ballinderry won the 2001 Derry Championship, once again defeating Bellaghy in the decider. The club went on to win the 2001 Ulster Club Championship with victories over St. Gall's in the quarter-final (after a replay), Cavan Gaels in the semi-final and Mayobridge in the final. Muldoon was awarded Ulster Football Award Winner at the AIB GAA Provincial Player Awards 2001 for his role in Ballinderry's march to claim the Ulster Club Championship. He was presented his award by GAA President Seán McCague. Ballinderry went on to represent Ulster in the All-Ireland Senior Club Football Championship, which they won defeating Tír Chonaill Gaels (London) in the quarter-final, Rathnew (Wicklow) in the semi-final and Nemo Rangers (Cork) in the final. Muldoon played through the pain barrier in the Championship, delaying an operation on a troublesome hip injury until after the All-Ireland final.