Murphy began his career at English side Manchester City. He spent spells out on loan at Oldham Athletic and Peterborough United but did not make a senior appearance at Manchester City before leaving to join Swansea City in 2003. He spent three seasons at Swansea before returning to his native Ireland to join Bohemian where he spent another three years. In November 2009 he returned to England to join Ipswich Town, where he spent two seasons before joining Queens Park Rangers in 2011. Murphy spent four seasons at Queens Park Rangers before leaving to join Portsmouth in 2015, where he spent one season, before joining Cardiff City in 2016, spending a further four seasons with Cardiff before once again returning to Ireland in 2020 to join Waterford.