Thwaites was married to Elaine Stanley, a hairdresser. The couple moved to Blackpool where they raised their daughter, Lindsey, and where Thwaites worked as a hospital porter. A nephew, Steve Lilwall, played League football for West Bromwich Albion. While on holiday in Port el Kantaoui, Tunisia, in June 2015, Thwaites and his wife were among those murdered in the Sousse attacks. A minute's silence was held in their memory on 1 August 2015 before Birmingham City's friendly game against Leicester City at St Andrew's.