Bourgeois was born in Paris, and was trained in law. After holding a subordinate office (1876) in the department of public works, he became successively prefect of the Tarn (1882) and the Haute-Garonne (1885), and then returned to Paris to enter the Ministry of the Interior. He became Prefect of Police in November 1887 at the critical moment of Jules Grévy's resignation from the presidency. In the following year, he entered the Chamber, being elected deputy for the Marne, in opposition to George Boulanger, and joined the Radical Left. He was undersecretary for Home Affairs in Charles Floquet's ministry of 1888 and resigned with it in 1889, being then returned to the chamber for Reims. In Pierre Tirard's ministry, which succeeded, he was Minister of the Interior, and subsequently, on 18 March 1890, Minister of Public Instruction in the cabinet of Charles Louis de Saulces de Freycinet, a post for which he had qualified himself by the attention he had given to educational matters. In this capacity, he was responsible for some important reforms in secondary education in 1890.

He retained his office in Émile Loubet's cabinet in 1892, and was Minister of Justice under Alex Andre Ribot at the end of that year, when the Panama scandals were making the office one of peculiar difficulty. He energetically pressed the Panama prosecution, so much so that he was accused of having put wrongful pressure on the wife of one of the defendants in order to procure evidence. To meet the charge, he resigned in March 1893 but again took office and retired only with the rest of the Freycinet ministry.

In November 1895, he formed his own cabinet, distinctively radical, which fell as the result of a constitutional crisis arising from the persistent refusal of the Senate to vote supply. He was an eminent Freemason and eight of his cabinet members were Freemasons.

The Bourgeois ministry seemed to think that popular opinion would enable them to override what they regarded as an unconstitutional action on the part of the upper house. However, the public was indifferent, and the Senate triumphed. The blow damaged Bourgeois's career as an homme de gouvernement. As Minister of Public Instruction in the Brisson cabinet of 1898, he organized courses for adults in primary education. After the short ministry, he represented his country with dignity and effect at the Hague Peace Convention, and in 1903 was nominated a member of the permanent court of arbitration.

He held somewhat aloof from the political struggles of the Waldeck-Rousseau and Combes ministries, travelling considerably in foreign countries. In 1902 and 1903, he was elected President of the Chamber. In 1905, he replaced the duc d'Audiffret-Pasquier as senator for the department of Marne, and in May 1906, he became Minister of Foreign Affairs in the Sarrien cabinet. He was responsible for the direction of French diplomacy in the conference at Algeciras. He was delegate to both Hague Conferences held in 1899 and 1907. Bourgeois also became delegate to Paris Peace Conference and strongly supported the Japanese Racial Equality Proposal as "an indisputable principle of justice".

Following World War I, he became President of the Council of the League of Nations and won the Nobel Peace Prize for his work in 1920.