Although born in Warsaw, Poland, Kubary spent much of his early life in Germany where he fled to escape civil unrest and persecution. In May 1863, Kubary worked for the Chief Administrator's office in Cracow Province, Austria. He then later worked as a tax collector for the Commissioner for the underground National Government. Within a year Kubary had quit his job and moved to Dresden, then back to Warsaw where he was arrested for his part in the Polish uprising. He was eventually released and fled back to Germany.

While in Hamburg, John Kubary met the founder of the Godeffroy Museum (which specialised in natural history and ethnography of the South Seas) and was offered a five year contract to collect specimens for the museum. Kubary's first trip was to Apia, Samoa in 1869 where he stayed for about six months. During this time he made trips to Fiji and Tonga, became interested in ornithology, learnt to speak Samoan and sent off his first collection of marine creatures and native mask casts to the Godeffroy Museum. In 1870 he sailed to the Ellice, Gilbert and Marshall Islands where he complied a dictionary of the vocabulary and grammar of the Ebon Islands dialect. He also produced his first publication which listed his exploration findings and included his hand-drawn maps and sketches. For the next four years Kubary went on collecting expeditions to many other islands including Yap, Palau, Ponape and Melanesia.

In 1875 Kubary arrived in Sydney, Australia on board the Mikado and immediately applied for naturalization, which he promptly received. Little is known about his work in Australia. Ten days after arriving, John Kubary sailed back to Germany and his contract with the Godeffroy Museum was extended for a further five years. He then returned to Mpomp, Ponape, where he built a permanent residence and established a plantation. From this island base he travelled to many more islands including Mortlock and Truk to continue his collections. But this soon stopped when the Godeffroy Museum ran out of money and had to terminate Kubary's contract.

With little income and no employment, John Kubary moved to Japan in 1882. For four months he worked at the Museums of Yokohama and Tokyo. Kubary returned to Ponape and continued topographical, geographical and geological surveys of the islands. In 1885 he was employed as an interpreter in Oceanic languages by the visiting German warship Albatross and later took charge of the German consul's plantation on the island of Matupi in New Britain. Eighteen months later Kubary was working as the manager of a trading station and plantation in New Guinea. He remained in New Guinea for much of his remaining life. A monument was erected in Ponape in his honour by German scientists in c1901.