In June 1898, he was elected president of the chamber, and was re-elected in 1901, but rejected in 1902. Nevertheless, he came forward brilliantly in 1904 and 1905 as a supporter of the law on the separation of church and state. He also gained a position on the Committee of Foreign Affairs, and was president of the committee when the Franco-German treaty of 1911 came before Parliament.
He was re-elected deputy in 1910, and on 23 May 1912 was chosen to be the President of the Chamber. In this role he played a great part during World War I as the national orator; he delivered orations more frequently than he made speeches. He served until he was elected President of France on 17 January 1920 by an overwhelming majority, having beaten Georges Clemenceau in the preliminary party ballot.
Deschanel aspired to a much more active role as president than had been de rigueur under the Third Republic; but, for reasons of his own mental health, was unable to put his ideas to the test.
As president, his eccentric behaviour caused some consternation; on one occasion, after a delegation of schoolgirls had presented him with a bouquet, he tossed the flowers back at them one by one. On another occasion he received the British Ambassador to France naked except for the ceremonial decorations of his office. It all culminated when, late one night, 24 May 1920, he fell out of a large window of the presidential train near Montargis after taking some sleeping pills and was found wandering in his nightshirt by a platelayer, who took him to the nearest level-crossing keeper's cottage. Soon afterwards, Deschanel walked out of a state meeting, straight into a lake, fully clothed. His resignation was offered on 21 September 1920, and he was placed in a sanatorium at Rueil-Malmaison for three months. After his release he was elected to the senate in January 1921, serving until his death.
Until the death penalty was abolished in 1981, he was the only French head of state during whose term in office no persons in France were executed. Deschanel himself was a longtime death penalty opponent.