He was of the wealthy cloth-maker Courthope family of Goddard's Green in Cranbrook, Kent, the son of Alexander Courthope and brother of the Peter Courthope who bought Danny House in Hurstpierpoint, Sussex and who was painted by Cornelius Johnson. He was left £200 in his father's will.
On December 25, 1616, he landed his ships, Swan and Defence, on Run, the smallest (~2 by 2.5 miles (3.2 km × 4.0 km)) of the Banda Islands, in a quest to break the Dutch hold on the nutmeg supply. He persuaded the islanders to enter an alliance with the British for nutmeg. After losing his two ships to mutiny and sinking by the Dutch, he fortified the island by erecting forts to overlook approaches from the east. With 39 men and the natives, with scarce food and water (springs of which the island is devoid of) supply, he proceeded to hold off a siege of the Dutch - who outnumbered them considerably - for over 1,540 days.
Despite numerous letters from the Company's directors allowing Courthope to leave his post, and even awarding him repeatedly for his efforts, he never gave in. Even after the fleet of Sir Thomas Dale sent from England to Run had been defeated by the Dutch governor of the archipelago, Jan Pieterszoon Coen, the decision never changed.
He was shot by the Dutch, who awaited him at night having received their spy's message, while rowing towards a nearby island in a small boat with several of his men in order to support resistance of the natives and to prepare them for a rebellion. Noticing the trap, he leapt into the sea and swam for it, dying en route.
The English departed without a struggle shortly after Courthope's death and their local allies - who considered themselves to be under His Majesty's reign - were being oppressed.
The author Giles Milton's book Nathaniel's Nutmeg: or, The True and Incredible Adventure of the Spice Trader Who Changed the Course of History, gives a vivid account of the struggle for possession of the Banda Islands.
- Milton, Giles (1999). Nathaniel's Nutmeg (reissue, illustrated ed.). Penguin Books. ISBN 978-0-14-029260-2. OCLC 44871451.
- "Nathaniel Courthope : Oxford Biography Index entry". Oxford Dictionary of National Biography. Oxford University Press. Retrieved 2010-08-12.
- Milton 1999.
- "Fortnightly Club of Redlands, California". RedlandsFortnightly.org. 2001-11-01. Retrieved 2010-08-12.
- Szulinski, Cathi (2009-04-30). "The First Russian Students in England". Krotov.info. Retrieved 2010-08-12.
- Ratnikas, Algirdas J. "Timeline Indonesia". Timelines.ws. Retrieved 2010-08-12.