His initial work in India was in dealing with fever and dysentery that affected the troops posted in the Ganjam district. During this posting, he described the birds of the Eastern Ghats. On 1 March 1837 he moved to the 2nd Light Cavalry and was posted at Trichinopoly and moved with the regiment to Jalnah in central India. He remained in the Deccan region for the next four years. In 1841 he visited the Nilgiri Hills on leave and in July of the same year he married Flora Alexandrina Matilda Macleod, niece of General Lewis Wentworth Watson. Flora had an interest in botanical art and took an interest in orchids. She was also an excellent guitarist. Around 1845 the Jerdon's lived in their Ooty home Woodside, (Woodside originally belonged to General Watson) and their children were baptised at the local St. Stephens church. Six months later he was appointed Civil Surgeon of Nellore. At Nellore, he interacted with the Yanadi tribes and obtained information on local names of birds and studied the natural history of the area. On 25 October 1844 he was transferred to Fort St. George as Garrison Assistant-Surgeon. During this time he took an interest in the fishes of the Bay of Bengal. On 12 February 1847 he was appointed Civil Surgeon of Tellicherry. This position led him to describe many species from the Malabar region including ants such as the distinctive Harpegnathos saltator. He resigned from civil charge on 3 June 1851 and was promoted as Surgeon with the 4th Light Cavalry in Sagar on 29 February 1852. After peace regained following the 1857 revolts, he was made Surgeon Major on 1 October 1858. He subsequently went to Darjeeling on sick leave and studied the Himalayan fauna before joining back into the 11th Native Infantry regiment in Burma and making use of that opportunity to study the region. Around 1861 a mission to Tibet was to be conducted by Captain E. Smythe and Jerdon was to accompany the group (which included Dr Stewart of the Saharanpur botanical garden; Capt. Bassevi, meteorologist; and Medlicott, geologist) as botanist but failure to obtain passports from Pekin led to the mission being cancelled. Around the same time Lord Canning enabled him to take special duty that would allow him to work on the publication of a series of books on the vertebrates of India. This began with his works on the Birds of India, followed by works on the mammals, reptiles and fish. On 28 February 1868 he retired from service and he was given the honorary position of Deputy Inspector-General of hospitals in Madras on 28 October 1868. While still in Gauhati, Assam he suffered a severe attack of fever and moved to Calcutta to convalesce but his condition deteriorated leading to his return to England in June 1870. In 1871 he became a member of the Berwickshire Natural History Society and joined them on walks. His health however continued to decline and he died at Aubyns Road, Upper Norwood on 12 June 1872, and was buried in West Norwood Cemetery. He discussed the birds of India with his friend Dresser even hours before his death. Flora died at her home in 40 Marina on 24 August 1910 and was buried at the Hastings Borough Cemetery.