Kokovtsov was admitted as a candidate for a civil service position in the Imperial Ministry of Justice serving first in the statistical, then the legislative and finally in the criminal office. From 1879 to 1890 he served as Senior Inspector and Assistant Head of the Central Administration of Prisons. This period is noted for its prison reforms formulated by State Secretary K.K. Grot a senior member of the Imperial State Council. From 1890 to 1896, he served in the State Council as Assistant State Secretary, State Secretary and finally as Assistant Imperial Secretary where he worked primarily on matters reviewed by the RussianImperial State Council's Department of State Economy. From 1896 to 1902 he served in one of the three Assistant Minister of Finance positions under Sergei Witte. After resigning from the position, he served as Imperial Secretary until his appointment as Minister of Finance in 1904. He resigned the next year when his former superior in the Finance Ministry, Witte, assumed the Chairmanship of the Council of Ministers. Although not a Minister, he then played a substantial role in securing a loan that did nothing less than keep the Imperial government from having to devalue its currency and leave the gold standard, then was the basis of almost all financially stable, secure and modern countries. Kokovtsov returned as Minister of Finance in the cabinets of Ivan Goremykin and Peter Stolypin. Kokovstov was an anti-Semite who believed the problem with Jews was not their 'backwardness' but the fact that they were 'so clever'. Kokovtsov succeeded Stolypin as Chairman of the Council of Ministers after Stolypin's assassination in 1911, while also maintaining his post as Minister of Finance, and held both offices until his retirement in 1914. Kokovtsov opposed to the appointment of Alexei Khvostov. In 1912 Kokovtsov asked the Tsar to authorize Grigori Rasputin's exile to Tobolsk. Nicholas refused: "I know Rasputin too well to believe all the tittle-tattle about him." Kokovtsov had offered Rasputin a substantial amount of money to leave for Siberia and ordered the newspapers not to mention his name in connection with the Empress. The Tsar dismissed Kokovtsov on 29 January 1914 for a "lack of control over the press". In domestic policy, Kokovtsov's time as Prime Minister saw the passage of two laws in 1912 that provided accident and sickness insurance to about 20% of workers.
Retirement and later life
Upon retiring, Kokovstov was invested with the title and rank of count. After the February Revolution, he moved to Kislovodsk. After the October Revolution of 1917 he was investigated by the Cheka, but escaped with his family to Finland and eventually settled in Paris. He was a leading figure in Russian émigré society until his death on 29 January 1943. In 1933 he published his memoirs, describing his childhood and education as well as his early years in government service life from 1903 till 1919.
Relationship with Sergei Witte
Witte states in his autobiography that while Kokovtsov was serving as one of his assistants, he was left alone to do the business he knew so well and that Kokovtsov was the source of several small but meaningful reforms in the finances of the Russian Empire. Much was made of Kokovtsov's differences with Witte which resulted in the two refusing to work with one another after 1905—06. The apparent cause of these differences were conflicts over courses of action in the preparation for peace talks with Japan, following the Russo-Japanese War; the changing of the government structure in the wake of widespread political unrest; Witte's opposition to several of Kokovtsov's policies as Minister of Finance during the Russo-Japanese War, and in an important loan negotiation that occurred in 1905—06. The differences were made public in the Council of State when one or the other would make comments in opposition to the other's viewpoint on various issues. Many historians have made the case that the differences were the result of Witte's desire to return to the Chairmanship of the Council of Ministers and his knowledge that his long-time associate was one of his chief rivals for the position. Some speculate that the differences were actually rather minor and overstate since both men, despite being in opposing political camps, could safeguard the financial reforms that they worked together to implement in the 1890s and early 1900s. It is known that Kokovtsov visited Witte in 1915 during the illness that led to Witte's death and that Witte offered Kokovtsov the position of State Controller, a ministerial post, in his govenment. He was awarded Order of the White Eagle and Order of Prince Danilo I.