His time in the post saw the first discussions on the introduction of police dogs to the force, but he is best remembered today for his championship of the method of fingerprinting to identify criminals.
He meanwhile took evening classes at University College, London, to prepare for the entrance examination of the Indian Civil Service, which he then passed on 9 July 1873.
He had already been exchanging letters with Francis Galton regarding the use of fingerprinting to identify criminals, either instead of or in addition to the anthropometric method of Alphonse Bertillon, which Henry introduced into the Bengal police department.
It was Haque who was primarily responsible for developing a mathematical formula to supplement Henry's idea of sorting in 1,024 pigeon holes based on fingerprint patterns.
Years later, both Haque and Bose, on Henry's recommendation, received recognition by the British Government for their contribution to the development of fingerprint classification.
The Henry Classification System quickly caught on with other police forces, and in July 1897 Victor Bruce, 9th Earl of Elgin, the Governor-General of India, decreed that fingerprinting should be made an official policy of the British Raj.
In the same year, while on leave in London, Henry spoke before the Home Office Belper Committee on the identification of criminals on the merits of Bertillonage and fingerprinting.
In 1901, Henry was recalled to Britain to take up the office of Assistant Commissioner (Crime) at Scotland Yard, in charge of the Criminal Investigation Department (CID).
He continued with his technological innovations, installing telephones in all divisional stations and standardising the use of police boxes, which Bradford had introduced as an experiment but never expanded upon.
On Wednesday 27 November 1912, while at his home in Kensington, Henry survived an assassination attempt by one Alfred (also reported as "Albert") Bowes, a disgruntled cab driver whose licence application had been refused.
Sir Edward appeared at court and followed a humane tradition of pleading for leniency for his attacker, stating that Bowes had wanted to better himself and earn a living to improve the lot of his widowed mother.
Feeling let down both by his men and by the government, whom he saw as encouraging trade unionism within the police (something he vehemently disagreed with), Henry immediately resigned on 31 August.
He continued to be involved in fingerprinting advances and was on the committee of the Athenaeum Club and the National Society for the Prevention of Cruelty to Children, as well as serving as a Justice of the Peace for Berkshire.
In April 1992, it was located in the cemetery adjoining All Souls Church, South Ascot by Metropolitan Police fingerprint expert Maurice Garvie & his wife Janis.