John T. O'Brien arrived in Buenos Aires in 1812 to open a merchant house. He enrolled in the army and fought in Uruguay with General Soler, being promoted to lieutenant. In 1816 O'Brien joined José de San Martin's mounted grenadiers regiment in the Andes army. After the battle of Chacabuco John T. O'Brien was promoted to captain and appointed aide-de-camp to general San Martin. O'Brien fought in the battles of Cancha Rayada and Maipú, and in the campaign of Peru. In 1821 he was promoted to colonel and awarded the "Orden del Sol" and Pizarro's golden canopy, which have been borne by the viceroys of Peru in processions.

In Peru John T. O'Brien turned his attention to the mining business. He received from the Peruvian government a grant for the silver mine of Salcedo, near Puno. O'Brien and his associate, Mr. Page, who represented Rundell & Bridge London jewellers, embarked in an effort to provide food and supplies to their miners at Lake Chiquito at 5,500 meters above sea level, from the port of Arica, located 380 kilometres away in the Pacific coast. They purchased a boat in Arica, stripped it of anchor and rigging and after two years of hard labour managed to launch her on the lake. This was the first attempt to establish regular communications between the valleys in Bolivia and the Pacific coast. Unfortunately for O'Brien and Page, a storm destroyed the vessel and with it the hopes of carrying on the mining works. Other remarkable efforts of O'Brien included the transportation of a steam engine across the Andes, digging through Laycayota mountain a canal 600 meters long traversed by nine locks, and laying a railroad for the conveyance of ore.

After the failure of his mining undertaking in Peru, John Thomond O'Brien returned to Buenos Aires. In the mid-1820s a group within the Irish elite of Buenos Aires, including doctors Michael O'Gorman and John Oughagan, and the Irish chaplain Fr. Moran, attracted the interest of the local government to implement an immigration scheme from Ireland to Buenos Aires. They communicated with the archbishop of Dublin and in 1826 commissioned O'Brien to travel to Europe and recruit "moral and industrious" immigrants. He spent two years in Ireland trying to engage emigrants without success. However, he met John Mooney of Streamstown, Co. Westmeath, who went to Argentina in 1828 when O'Brien was returning. This was to be the start of the Irish emigration to Argentina from the Westmeath-Longford-Offaly area. In addition to John Mooney, his sister, Mary Bookey (née Mooney) and her husband, Patrick Bookey, went with O'Brien.

Back in South America in 1835, O'Brien was promoted to general in Peru. In Buenos Aires, he fell in disgrace of the regime led by Juan Manuel de Rosas and was imprisoned before being released through a combination of pleading by Rosas's daughter and British diplomatic pressure.

In 1845 John T. O'Brien published in London the pamphlet Correspondence with the British Government relative to the war between Buenos Ayres and Montevideo and the free navigation of the River Plate, with an Appendix detailing some of the acts committed by Rosas, Governor of Buenos Ayres (London: Reynell & Weight, 1845). In 1847 he was in Montevideo and the following year was appointed special envoy of the Uruguayan Republic to the United Kingdom.

John Thomond O'Brien returned to Ireland and died on 1 June 1861 in Lisbon, on his way back to South America. His remains were repatriated to Argentina in 1938 and received an official funeral. A town in Bragado was named after him.