Prafulla Chandra was born on 2 August 1861 in Raruli-Katipara, a village in the District of Khulna (in present day Bangladesh). His early education started in his village school. He often played truant and spent his time resting comfortably on the branch of a tree, hidden under its leaves. After attending the village school, he went to Kolkata, where he studied at Hare School and the Metropolitan College. The lectures of Alexander Pedler in the Presidency College, which he used to attend, attracted him to chemistry, although his first love was literature. He continued to take interest in literature, and taught himself Latin and French at home. After obtaining a F.A. diploma from the University of Calcutta, he proceeded to the University of Edinburgh on a Gilchrist scholarship where he obtained both his B.Sc. and D.Sc. degrees.

In 1888, Prafulla Chandra made his journey home to India. Initially he spent a year working with his famous friend Jagadish Chandra Bose in his laboratory. In 1889, Prafulla Chandra was appointed an Assistant Professor of Chemistry in the Presidency College, Kolkata. His publications on mercurous nitrite and its derivatives brought him recognition from all over the world. Equally important was his role as a teacher - he inspired a generation of young chemists in India thereby building up an Indian school of chemistry. Famous Indian scientists like Meghnad Saha and Shanti Swarup Bhatnagar were among his students.

Prafulla Chandra believed that the progress of India could be achieved only by industrialization. He set up the first chemical factory in India, with very minimal resources, working from his home. In 1901, this pioneering effort resulted in the formation of the Bengal Chemical and Pharmaceutical Works Ltd.