In 1844 Pleydell-Bouverie was returned to Parliament for Kilmarnock Burghs, a constituency he represented until 1874. He served as Under-Secretary of State for the Home Department in Lord John Russell's first administration from July 1850 to March 1852, and from April 1853 to March 1855 he was Chairman of Committeesof the House of Commons, while Lord Aberdeen was prime minister. In March 1855, when Lord Palmerston became premier, Pleydell-Bouverie was made Paymaster-General and Vice-President of the Board of Trade, and sworn of the Privy Council. In August of the same year he was transferred to the Presidency of the Poor Law Board, a position he held until 1858. However, he was never a member of the cabinet. In 1857 he was appointed one of the committee of the Council on Education. He was Second Church Estate Commissioner from August 1859 to November 1865, and from 1869 he was one of the Ecclesiastical Commissioners for England. Though a staunch liberal, Pleydell-Bouverie belonged to the old whig school, and during his last years in parliament often found himself in disagreement with the policies of Liberal prime minister, William Ewart Gladstone. In 1872, when a charge of evasion of the law was made against Gladstone in connection with the appointment he made to the rectory of Ewelme, Pleydell-Bouverie expressed regret "We all have our amusements at various times, but that of the right hon. Gentleman, when he has nothing else to do, is to drive coaches and six through Acts of Parliament". When the Irish University Bill was introduced in March, Pleydell-Bouverie finally broke with Gladstone. He denounced the measure as miserably bad and scandalously inadequate to its professed object. He voted against the second reading on 10 March, when the government was defeated. Subsequently, in letters addressed to The Times he continued his attacks on the measure and on its framers. After his retirement from parliament in 1874, Pleydell-Bouverie became in 1877 associated with the Corporation of Foreign Bondholders, and was soon made its chairman. Under his guidance the debts of many countries were readjusted, and the corporation's scheme for dealing with the Turkish debt was confirmed by the sultan's iradé of January 1882. Bouverie was Deputy Chairman of the Mersey Railway at its opening in 1886. He was also director of the Great Western Railway Company and of the Peninsular and Oriental Steam Navigation Company. He addressed numerous letters to The Times newspaper under the signature of "E. P. B." He was appointed High Sheriff of Wiltshire for 1882–83.
