From 1978 to 1988 he worked as an economist, researcher and deputy head of a department at the Foreign Ministry of Mongolia. From 1988 to 1990 he worked as a specialist at the Ministry of Foreign Economic Relations and Trade and in the meantime, he was a director of a market research institute.
From 1990 to 1992 he held a seat in the State Small Khural (parliament) for the first time, representing the Mongolian Democratic Party and chaired a standing committee in the parliament. From 1992 to 1993 he held a seat in the State Great Khural (parliament) representing the Mongolian Democratic Party. He was appointed as a president of the Academy for Political Education in 1992.
After that he served as the chairman of the common elections commission of Mongolian National Democratic Party and Mongolian Social Democratic Party for the presidential elections of June 6 1993. From 1993 to 1996 he worked as the chairman of the Presidential office for Punsalmaagiyn Ochirbat, first official president of Mongolia.
This made Enkhsaikhan the first prime minister since the 1920s who wasn't a member of the Mongolian People's Revolutionary Party (MPRP). He presided over a period of aggressive economic reforms, including housing privatization, acceleration of other privatization programs, liberalization of most remaining controlled prices, closure of insolvent banks and elimination of duties on imports. Mongolian relations with international organizations such as the International Monetary Fund and World Bank, which had been strained due to slow reforms under the previous regime, were now strengthened. The parliamentary majority of Democratic Party (DP) and Mongolian Social Democratic Party forced him to resign in April, 1998, because of tensions between him and other leaders in the Coalition. He was then replaced by Tsakhiagiyn Elbegdorj (DP).
In 2005 Enkhsaikhan ran for the presidential elections from Mongolian Democratic Party , but received less than 20% of the votes and lost against Nambaryn Enkhbayar (MPRP).
When Enkhsaikhan worked as a chairman of Mongolian Democratic Party he moved to form a coalition with Motherland Party. It is said that many members of Democratic Party opposed it because Motherland Party was a "one-person's company party" whose chairman Badarchiyn Erdenebat is a chairman of private Erel company that digs gold in Mongolia. In addition, Motherland Party had only one member of Parliament that is Badarchiyn Erdenebat in its history until 2004.
The coalition with the Motherland Party was a failure in the parliamentary elections in 2004. Three of the Democratic Party members were elected to the parliament as individuals because they were not offered slots in the coalition candidates. He became a member of parliament in 2004 from Democratic Party. The coalition and its foe former communist MPRP won even split votes.
The coalition government was established with agreements of all parties involved. Motherland Party was given two seats at the Government Cabinet of the grand coalition government for its 7 elected MPs vs. Democratic Party's 25 elected MPs and Civil Will Party's MPs. However, Badarchiyn Erdenebat, Enkhsaikhan's elevated ally wanted Prime Ministership and one more seat at the Government Cabinet. When it was not agreed by all participating parties of the Motherland Democracy Coalition, Badarchiyn Erdenebat announced the dissolution of the coalition at the parliament without consent of the coalition parties. According to Mongolian law, if someone announces anything at the parliament, it becomes valid without need of vote for this case. Mendsaikhan Enkhsaikhan joined Badarchiyn Erdenebat to dissolve Motherland Democracy Coalition to join MPRP to establish new coalition with MPRP for bigger position at the government.
In January 2006 he voted with MPRP members for the dismissal of Elbegdorj's government. He did so in spite of a decision of the Democratic Party's Directing Board, not to vote against its own coalition government. The Party's Main Legal Committee therefore cancelled Enkhsaikhan's membership in February.