In 1832, Falconer became Superintendent of the Saharanpur botanical garden, India, succeeding John Royle.
Falconer remained at Saharanpur until 1842, during which time he became widely known for his study of fossil mammals in the Siwalik Hills.

Falconer and his associates may have made the first discovery of a fossil ape, in the 1830s in the Neogene deposits in the Siwalik Hills.
In the Tertiary strata of the Siwalik Hills in 1831 Falconer discovered bones of crocodiles, tortoises and other animals.
 With others, he later brought to light a sub-tropical fossil fauna of unexampled extent and richness, including remains of Mastodon, the colossal ruminant Sivatherium, and the enormous extinct tortoise Colossochelys Atlas.
Falconer also published a geological description of the Siwálik Hills in 1834.
For these valuable discoveries he and Proby Cautley (1802–1871) together received the Wollaston Medal from the Geological Society of London, its highest award, in 1837.

In 1834 Falconer was asked by a Commission of Bengal to investigate the commercial feasibility of growing tea in India.
On his recommendation tea plants were introduced, and the resultant black tea became competitive with Chinese teas.

Falconer returned from India in 1842 because of ill health.
 He brought back 70 large chests of dried plants and 48 cases of fossils, bones and geological specimens.
He then travelled throughout Europe making geological observations, and was elected Fellow of the Royal Society in 1845.
Continuing in the service of the British East India Company as a naturalist, he pursued research at the British Museum and East India House and prepared casts of the most remarkable fossils for the leading museums of Europe.
In 1832, Falconer became Superintendent of the Saharanpur botanical garden, India, succeeding John Royle. Falconer remained at Saharanpur until 1842, during which time he became widely known for his study of fossil mammals in the Siwalik Hills. 
Falconer and his associates may have made the first discovery of a fossil ape, in the 1830s in the Neogene deposits in the Siwalik Hills. In the Tertiary strata of the Siwalik Hills in 1831 Falconer discovered bones of crocodiles, tortoises and other animals.  With others, he later brought to light a sub-tropical fossil fauna of unexampled extent and richness, including remains of Mastodon, the colossal ruminant Sivatherium, and the enormous extinct tortoise Colossochelys Atlas. Falconer also published a geological description of the Siwálik Hills in 1834. For these valuable discoveries he and Proby Cautley (1802–1871) together received the Wollaston Medal from the Geological Society of London, its highest award, in 1837.
In 1834 Falconer was asked by a Commission of Bengal to investigate the commercial feasibility of growing tea in India. On his recommendation tea plants were introduced, and the resultant black tea became competitive with Chinese teas.
Falconer returned from India in 1842 because of ill health.  He brought back 70 large chests of dried plants and 48 cases of fossils, bones and geological specimens. He then travelled throughout Europe making geological observations, and was elected Fellow of the Royal Society in 1845. Continuing in the service of the British East India Company as a naturalist, he pursued research at the British Museum and East India House and prepared casts of the most remarkable fossils for the leading museums of Europe.
Hugh Falconer