In 1896, he was elected to the House of Commons as an independent Liberal, but resigned in 1899 to protest against the sending of Canadian troops to the Boer War. He was re-elected soon after his resignation. He argued that Prime Minister Wilfrid Laurier was "un vendu" ("a sell-out") to British imperialism and its supporters in Canada.
To counter what he perceived to be the evils of imperialism, in 1903 he created the Nationalist League (Ligue Nationaliste) to instill a panCanadian nationalist spirit in the Francophone population. The League opposed political dependence on both Britain and the United States, supporting instead Canadian autonomy within the British Empire.
Bourassa left the federal government in 1907 but remained active in Quebec politics. He continued to criticize Laurier, opposing Laurier's attempts to build a Canadian navy in 1911, which he believed would draw Canada into future imperial wars between Britain and Germany. He supported the eventual creation of an independent navy, but did not want it to be under British command, as Laurier had planned. This lack of support helped cause Laurier and the Liberals to lose the 1911 election.
In 1913 Bourassa denounced the government of Ontario as "more Prussian than Prussia" during the Ontario Schools Question crisis, after Ontario restricted the use of French in their schools and made English the official language of instruction.
Bourassa led French Canadian opposition to participation in World War I, especially Robert Borden's plans for conscription in 1917. He could agree that the war was necessary for the survival of France and Britain, but felt that only those Canadians who volunteered for service should be sent to the battlefields of Europe. He also opposed conscription in World War II, though less effectively.
His influence on Quebec's politics can still be in seen today in all major provincial parties.