Born on 17 March 1787 to Charles and Ann Fergusson, Fergusson was commissioned as ensign in 1801, in the 18th (Royal Irish) Regiment of Foot, before transferring to the 43rd (Monmouthshire) Regiment of Foot, training as light infantry under Sir John Moore at Shorncliffe. Promoted lieutenant in 1804, and captain in 1806, he served in the Light Division throughout the Peninsular War. Fergusson was present at the battles of Roliça, Vimeiro, (where he sustained wounds), and Corunna, where his regiment formed part of the reserve. Fergusson accompanied the 43rd on the 1809 Walcheren Expedition before returning to the Peninsula, experiencing action at River Côa, Bussaco, Sabugal, Fuentes de Onoro, as well as Ciudad Rodrigo and Badajoz, where he formed part of the 43rd's storming parties, receiving wounds both times. He received a gold medal for his action at Badajoz. Following fine action at Salamanca in 1812 he was promoted to Major without purchase, taking a post in the 79th Foot. He exchanged into the 85th Foot, seeing action at Bidassoa, Nivelle, Nive and Bayonne.