Pyotr Vologodsky was born in Yenisei governorate into a family of a priest. He entered the Faculty of Law of St. Petersburg University but was excluded for his involvement in political activities. He passed the exams for the course of the Law faculty of Kharkiv University as an external student (1892). In the 1880–1890s, we worked in Siberian judicial institutions and later took up private practice as a lawyer. He came to prominence after the trials of 1905–1907 (during the revolution), in which he acted as a lawyer for protestors. In 1901–1917, he was elected as a deputy of the Tomsk City Duma, and later as an MP of the 2nd State Duma (which had been dissolved before he arrived in the capital). Vologodsky took part in the Siberian oblast movement (Siberian regionalism) for the autonomy of Siberia. He collaborated with the Socialist Revolutionary Party (SRs) in Tomsk.

After the February Revolution, Vologodsky became a member of the governorate commissariat for the administration of the Tomsk governorate, in August he was elected as the senior chairman of the Omsk judicial chamber.

In January 1918, he was elected to the Provisional Siberian Government and appointed Minister of Foreign Affairs. After the government led by Pyotr Derber moved to the Far East, he remained in Omsk. In the spring of 1918, he was elected as the Honorary Chairman of the Siberian Cossack Host Court.

In June 1918, after the overthrow of the Soviet regime in the region, he headed the Provisional Siberian Government. The autumn of 1918 saw him become a member of the Provisional All-Russian Government (Ufa Directorate). In September–October 1918, he made a trip to Transbaikalia and the Far East to obtain subjugation of the local political entities and obtain diplomatic recognition, financial and military support from the allies. In Chita, he met the ataman Grigory Semyonov.

In November 1918, Vologodsky was elected the Chairman of the All-Russian Council of Ministers, a newly formed executive body of the Directorate. After Aleksander Kolchak came to power, he resigned but accepted the post of Chairman of the Council of Ministers in the new Russian Government of Aleksander Kolchak (November 1918 to November 1919). In December 1918, he was the interim Minister of Foreign Affairs.

The winter of 1919–1920 saw him emigrate to China. He worked in the legal department of the Chinese Eastern Railway (СЕR) in Harbin but lost his job after the conclusion of a new USSR-Chinese agreement on the Chinese Eastern Railway (1924). He fell ill with a nervous breakdown and died in 1925 in Harbin at the Red Cross Hospital for the Poor.