Murphy signed for Scunthorpe United in May 2006 after being released by Sunderland. He had an excellent 2006–07 season, and was an integral part of the team that led Scunthorpe to the League One trophy. He was in the League One team of the season, and also won the golden glove (award for most clean sheets). He was also named League One player of the month for February 2007. On top of this, he hit the crossbar during Soccer AM's crossbar challenge. His clean sheet in Scunthorpe's 2–0 home victory over Burnley on 30 September 2007 earned him a place in the Championship Team of the Week. He made the Team of the Week once more following his side's 1–0 victory over Charlton Athletic in February.