Before the 2001–02 season, Hughes featured as Newcastle reached the final of that summer's UEFA Intertoto Cup. In the semi-final first leg away to 1860 Munich at the Olympiastadion, he headed in Wayne Quinn's cross in the 83rd minute to win the match 3–2. In the second leg of the final on 21 August, he scored a last-minute equaliser for a 4–4 draw against Troyes, but his team lost on the away goals rule. On 27 January 2002, he confirmed a 4–2 win at Peterborough United in the fourth round of the FA Cup, again heading in a cross from Quinn. In August 2003 he missed the crucial penalty in the shootout as Newcastle lost in the final qualifying round for the 2003–04 Champions League.