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Moorcroft was born in Lancashire and educated in Liverpool for the medical profession. While he was a student he was assigned to examine a local outbreak of cattle disease, as a result of which he switched to veterinary science. After amassing a considerable fortune in London he lost his wealth through the filing of numerous bad patents and in 1808 he took a position as veterinary surgeon with the Bengal Army. During this time he also took the position of Superintendent of the East India Company's stud.
He travelled widely in central Asia and became the first British traveller to cross the Himalayas. Falling out of favour with the Bengal Army for spending too much time in the Himalayan region he undertook a journey for trade to Kabul. On returning from Kabul in 1823 Moorcroft died and was taken to Balkh where he was buried outside the city walls.