Gan was of Hokkien Chinese descent, born and educated in Melaka, and the eldest son of five in his family. His forefathers emigrated from Fujian Province, China to Malaya. Owing to poor circumstances, he probably had an elementary school education in which he learnt to read and write in simple English and keep accounts. After his father's death, sixteen year old Gan was involved in the nutmeg business on a very small scale.
Later, he was taken on as an apprentice by Messrs. Guthrie and Company. Gan was diligent and capable, and his ability won him the recognition and keen interest of Thomas Scott, one of the partners in the company. Scott was one of the early British pioneers responsible for developing Tanjung Pagar and the port of Singapore. Eventually, Gan was promoted to the post of Assistant Storekeeper and then Chief Storekeeper of the company. In 1874, he became the company's Chief Compradore, a position which he held for the next 25 years. Thomas Scott later helped to finance some of Gan's early business ventures, one of which was to supply labour and transport to the Tanjong Pagar Dock Company which helped Gan to make most of his personal fortunes.
Gan married his first wife, Koh Chwee Neo, at the age of eighteen and in 1859 adopted his first son, Gan Tiang Tock, who was an important partner in the building of his fortune. He had in total five wives, seven sons and two daughters. However, only two of his children were born by his wives; his other children were mostly adopted, a customary practice which was then considered auspicious. His immediate family members were: Wives: 1. Kho Chwee Neo 2. Kho Eng Geok 3. Choo Ah Teng 4. Lim Neo Chick 5. Teo Bok Neo (China)Sons: 1. Gan Tiang Tok (Adopted) 2. Gan Tiang Keng (Adopted) 3. Gan Tiang Leong (Adopted) 4. Gan Tiang Khay (Adopted) 5. Gan Tiang Poh (Adopted) 6. Gan Tiang Choon (Adopted) 7. Gan Tiang Kwee (Born to 2nd wife, Kho Eng Geok) | Sisters: 1. Gan Gin Neo