Pratt was the son of a secretary to the Church Missionary Society; after graduating from Cambridge University in 1833 he went to India as a chaplain with the East India Company. In 1850 he became archdeacon of Calcutta.

An amateur scientist, Pratt became interested in geophysics and in 1854 his most important work was published when he formulated the theory of isostasy. While conducting his triangulation of India the surveyor, George Everest, found a discrepancy in the astrogeodetic and triangulation measurements between two stations – Kaliana and Kalianpur – near the Himalayas. From this Pratt surmised that mountain ranges failed to exert the gravitational pull expected of them and thus distorted measurements made with pendulums. He saw the Himalayas as having a lesser density than the crust below, and generalized that the higher the mountain range, the lower is its density. He compared the raising of mountains to fermenting dough in which the density decreases as the dough rises.

Some of the same ideas were present in a paper submitted just six weeks after Pratt's by George Airy although Airy preferred the image of an iceberg to that of rising dough.

Pratt wrote Mathematical Principles of Mechanical Philosophy (1836), a work that was expanded to On Attractions, Laplace's Functions, and The Figure of the Earth (1860, 1861, 1865).