Born on 8 April 1849, Cowie was the oldest of four children of the flax producer David Cowie (1825–1896) and Ann Cowie (1819–1906) in Scotland, where his mother ancestors had lived for generations. His three siblings were Mary, Andson and Edward.^[2][3]

The family moves to Arbroath on the Scottish east coast. His father was a director in the Wardmill Works of M.C. Thomson & Co., and Cowie trained as an engineer.^[4] He received private lessons with the aim of following his grandfather, an engineer in one of the first mills in Scotland.^[3]

Around 1873, Cowie married Flora Davidson. They had two children; Flora de Cruz (born 1874) and William Anson Edward Cowie de Cruz (born 1875).^[2] His wife died suddenly, aged 25, shortly after the birth of their second child. Cowie then married Amy Constance Pead, and they had two children; Muara Gladys (born 1888) and Andson Gordon (born 1891).^[2]

From April 1870, Cowie was hired as the chief engineer of Argyle under Captain Peter Orr and left Glasgow for Singapore on his 21st birthday.^[4] He then began to lead life as an adventurer in the pirate-infested waters of the Malay Archipelago. His career as chief engineer for Argyle ended at the end of 1872 when he was hired by Carl Schomburgk as captain of the Far East, and was commissioned to break the Spanish naval blockade to deal with the Sultan of Sulu, who ruled parts of the northern Borneo. His successful efforts forged a deep friendship with the Sultan of Sulu.^[5][6]

Cowie convinced the Sultan that to achieve a lasting success in overcoming the Spanish blockade he would need access to a safe harbour; from there he could wait until the shipping route to Sulu was free from Spanish warships. The Sultan permitted Cowie to build a port for his goods at Timbang Island in Sandakan, creating a British presence in Borneo. Cowie, along with two friends – Carl Schomburgk and John Dill Ross – founded the Labuan Trading Company, whose main task was to evade the Spanish naval blockade and bring weapons, opium, tobacco and goods to Sulu. No company ships were ever caught by the Spaniards.

In 1878, Baron von Overbeck and Alfred Dent approached Cowie knowing he has friendly with the Sultan of Sulu, asking for help in arranging land concessions in Borneo. Cowie agreed as he had plans to occupy territory as part of the British Empire. As the political situation was favourable to unilateral treaties, Cowie told the Sultan to leave the Spaniards to his country, helping foreign powers to take parts of the Sultan territory while expecting the Spanish would wish to avoid diplomatic involvement with the interests of other colonial powers. Cowie managed to get the Sultan to surrender his lands in north-eastern Borneo on 22 January 1878 for an annual payment of £1,000; which was later given to Overbeck and Dent as they received the full power of government and territorial rights to the possessions in Borneo, including the islands. The rights from this treaty were then transferred to the newly-founded British North Borneo Company in 1881.

In March 1882, Cowie purchased a 40 year-concession for the exploitation of coal fields in Muara in Brunei and founded Cowie Brothers, based in Singapore. From Labuan, he rented a shipyard for 99 years from which he shipped his coal. On 12 July 1887, Cowie handed over his franchise rights to the British North Borneo Company and returned with his family to England. Charles Brooke, who later acquired the mine, renamed it as "Brooketon" (today's Brooke Town).

In 1887, Cowie, together with Edmund Ernest Everett, was commissioned to conduct the company's business in Borneo. Due to the lack of transportation to move goods in the island, Cowie sought a concession to build a rail network from the West Coast Division to Sandakan. The company initially agreed and appointed Cowie as the Supervisory Board in 1894. In 1896 construction of the North Borneo Railway began but financial difficulties prevented the company fully connecting to northern Borneo; Cowie was unable to raise the necessary funds especially after company officials refused to borrow more money.^[7]

In 1893, under the patronage of Cowie and his brother Andson, a dictionary for the Sulu and Malay languages was created.^[8]

He was appreciated for his extensive knowledge of the territory and the people of Borneo. He rose to the position of Director General in 1897. In North Borneo in 1898 he met with Mat Salleh to bring an indefinite solution of the so-called Mat Salleh Rebellion.^[9] On 15 October 1909, after the retirement of Charles Jessel, he became Chairman of the Supervisory Board.^[1]

Toward the end of his life, Cowie suffered from heart disease. In July 1910, he travelled to Germany to undergo surgery. After his condition worsened, Cowie died on 14 September 1910 in Bad Nauheim.^[10] His body was returned to England and he was buried on 23 September in Charlton cemetery, near to his home, Mayfield, in Blackheath Park, Blackheath. His gravestone reads:

Although he was praised by the British Empire for his role in expanding the empire's influence, Cowie remains a key figure in the genesis of the North Borneo Dispute. To date, the North Borneo or the Sabah region in present day Malaysia remains a contentious issue. The region has led to a long-standing territorial dispute between Malaysia and the Philippines over much of the eastern part of Sabah, which known as North Borneo prior to the formation of the Malaysian federation.

Philippines maintains that it the successor state of the Sultanate of Sulu, claiming that the territory was only leased to the British North Borneo Company in 1878.

More recently, the region has garnered international attention again with the Malaysia-Sulu case, in which purported heirs of the last sultan of Sulu initiated an arbitration appeal against Malaysia. The claimants demanded $32 billion in compensation for what is said was illegal exploitation of the region's natural resources. Spanish arbitrator Gonzalo Stampa announced a settlement of almost $15 billion in favour of the claimants through the Paris Court of Appeal in 2022.^[11][12] The award was eventually struck down by the International Court of Justice in 2023.^[13]

• Volker Schult (2008). Wunsch und Wirklichkeit: deutsch-philippinische Beziehungen im Kontext globaler Verflechtungen 1860–1945 (in German). Logos Verlag Berlin GmbH. ISBN 978-3-8325-1898-1.
• K. G. Tregonning (1965). A History of Modern Sabah (North Borneo, 1881–1963). University of Singapore.