Harrington was Colonel of the Westminster Trained Bands (the Red Regiment) in 1642, and he commanded a London brigade (his own regiment, together with the Green Auxiliary Trained Bands of London and the Tower Hamlets Auxiliaries (the Yellow Regiment)) in Sir William Waller's Parliamentarian army at the Siege of Basing House and Battle of Alton in late 1643. As a Major-General, Harrington led out another brigade of suburban Trained Bands (the Tower Hamlets Regiment, the Southwark White Auxiliaries and the Westminster Yellow Auxiliaries) to join Waller in the campaign that culminated at the Battle of Cropredy Bridge on 29 June 1644. For the great combination of Parliamentary armies in the autumn of 1644, London provided a fresh brigade of five regiments under Harrington. It fought at the Second Battle of Newbury, where Harrington had his horse shot under him.