Educated at the Royal Grammar School, Guildford, he obtained an ensigncy by purchase in the old 95th Foot in 1780, and served under Major Francis Peirson during the January 1781 Battle of Jersey.

Le Couteur described his campaigns in Letters, Chiefly from India, giving an Account of the Military Transactions on the Coast of Malabar during the late War (1790).

When the island was returned to the Dutch after the peace in 1815, the legislative bodies, the inhabitants, and Spanish refugees presented Le Couteur with addresses acknowledging the important services he had rendered to the colony.

Le Couteur declined the Duke of York's offer to recommend him for command of a regiment, claiming he did not feel entitled to the honour as long as Peninsular officers remained unprovided for.

The younger John Le Couteur also dabbled in agricultural science in later life, was elected as a Fellow of the Royal Society in 1843, and served as an aide-de-camp to William IV and Victoria.