His father originally apprenticed him to a printer in Calcutta but hating the life he ran away after three days. Because of his Indian heritage, Skinner was unable to serve as an officer in the East India Company army and, at the age of sixteen, he entered the Maratha army as an ensign under Benoît de Boigne, the French commander of Maharaja Scindia's forces of Gwalior State. Boigne was impressed by his family ancestry, Skinners having served William the Conqueror in the 11th century. Once taken in, Skinner soon showed military talent. He remained in the same service under Pierre Cuillier-Perron, who became commander-in-chief of Sindhia's army after Boigne's retirement, until 1803, when, on the outbreak of the Second Anglo-Maratha War, all Anglo-Indians were dismissed from Maratha service.