Appointed governor of the provinces of Grodno (1902) and Saratov (1903), Stolypin demonstrated his concern for improving the welfare of the peasants as well as his firmness and efficiency in subduing their rebellions. Consequently, he gained the favour of Emperor Nicholas II and was appointed minister of the interior in May 1906. In July he was also named president of the Council of Ministers (i.e., prime minister).

Dismissing the first Duma (the elected legislative body created after the 1905 Revolution) on July 22 (July 9, O.S.), 1906, because it demanded a determining voice in the formulation of an agrarian reform program, Stolypin, by executive decree, introduced his own reforms. These gave the peasantry greater freedom in the selection of their representatives to the zemstvo (local government) councils, removed restrictions that had excluded the peasantry from participating in normal judicial procedures, and, most importantly, provided them with an opportunity to leave their communes, acquire private ownership of consolidated plots of land, and transform themselves, according to Stolypin's wish, into a prosperous, stable, and loyally conservative class of farmers (October and November 1906).

Stolypin, however, also instituted a network of courts-martial, which were authorized to try accused rebels and terrorists; within the few months of their existence they used “Stolypin's necktie” (the noose) to execute several thousand defendants; the prime minister gained the enmity of the left wing and much of the centre. He also provoked the opposition of the moderate left when he swiftly dismissed the second Duma (which met from March to June 1907) because it refused to endorse his agrarian reform proposals and when, on the day of its dissolution (June 16 【June 3, O.S.】, 1907), he issued—in complete disregard for the recently adopted constitution—a new electoral law reflecting his personal conservatism and Russian nationalism and restricting the franchise of the peasant and worker electorate as well as that of the national minorities.

Although he had earlier also alienated the extreme right by partially accepting the constitutional framework, Stolypin did obtain the cooperation of the party of the moderate right (the Octobrists), which dominated the third Duma (convened November 1907). With the Octobrists' aid he passed legislation confirming and elaborating his 1906 agrarian reforms (June 1910 and June 1911). He was also able to reimpose harsh Russification policies on Finland. When he convinced the Emperor to temporarily suspend both the Duma and the upper legislative house (the State Council) in order to bypass them and enact legislation on the extension of the zemstvo system into the Polish regions of the empire (March 1911), he also alienated the moderate right, which condemned him for once again abusing the constitutional system of government.

It is probable that Nicholas was considering his dismissal when Stolypin, while attending an operatic performance with the Emperor, was fatally shot (Sept. 14 【Sept. 1, O.S.】, 1911) by Dmitry Bogrov, a revolutionary who had used his police connections to gain admittance to the theatre.