After losing Leverkusen's nets to the young René Adler during the 2006–07 season, Butt decided to cancel the contract that linked him to the club until 2009, activating a clause that allowed him to leave the club should he fail to appear in more than half of the games during the second half of the campaign. In July 2007, he signed a two-year deal with Portuguese club S.L. Benfica.
Butt made his Eagles debut in the summer tournament of Torneio de Guadiana, held between Benfica, Sporting Clube de Portugal and Real Betis. In the competition, he saved a penalty against Betis, helping Benfica with the final win. At the Lisbon outfit, however, he played understudy to Portuguese international Quim, being used in the domestic cup matches. He only made one league appearance for Benfica, coming on as a substitute after Quim was sent off against C.S. Marítimo in October 2007 – in this match, he saved a penalty from Ariza Makukula with his first touch of the game, and his team eventually won 2–1.