Williams was appointed manager of Leyton Orient in February 2009. He started very well and managed to help Orient to 7 wins from his first 9 games in charge, including wins over teams such as Crewe Alexandra, Brighton & Hove Albion and Carlisle United. He led the relegation-threatened O's to an eventual mid-table finish of 14th place, retaining their League One status with several games to spare. After a poor run of form in March, Williams left Orient only hours after the side's 3–1 home defeat to Hartlepool United.