He quickly acquired a large practice in the equity courts, and through the influence of his father was appointed standing counsel to the Bank of England.

In 1866, he took silk and attached himself to the court of Vice-chancellor (Sir) Richard Malins, where he shared the leadership with Mr. W. B. Glasse.

Among the important cases in which he was engaged were the liquidation of Overend, Gurney, & Co.; the King of Hanover v. the Bank of England; Rubery v. Grant; Dr.Hayman v. the Governors of Rugby School; and the Republic of Costa Rica v. Erlanger.

His father's Wallwood estate was sold off posthumously in 1874, but Henry Cotton set aside and donated a plot of land upon which St. Andrew's Church in Leytonstone was built.

[5][6] His youngest son Hugh Benjamin Cotton (1871–1895) was featured in a Vanity Fair caricature on 15 March 1894 as president of the Oxford University Boat Club, but died of lung illness the following year in Davos Platz, Switzerland.