Following the 2013 Czech legislative election, Sobotka was appointed prime minister on 17 January 2014 by President Miloš Zeman.

His government introduced a series of measures to tackle tax evasion, such as electronic registration of sales or a VAT control system, strengthened relations with China, reformed the police, repealed the Civil Service Act, and enforced the smoking ban.

He also frequently clashed with President Miloš Zeman regarding the Russian intervention in Ukraine and resulting sanctions, domestic policy and Sobotka's withdrawn resignation in May 2017.

Sobotka is the first prime minister in 15 years and the third in the history of the Czech Republic to finish his full term.

On 14 June 2017, Sobotka announced his resignation as Leader of ČSSD due to low opinion polling prior to the 2017 legislative election but opted to stay on as prime minister.

As the finance minister, Sobotka formed an advisory body of economists, later becoming the National Economic Council of the Czech government.

[citation needed] Sobotka then served as interim leader of ČSSD after the resignation of Jiří Paroubek following the election.

His cabinet consisted of members of the coalition government – the ČSSD, ANO 2011, and Christian and Democratic Union–Czechoslovak People's Party.

Bohuslav Sobotka's views on the Czech Republic's membership in the European Union as prime minister were relatively positive.

[6] However, in early 2016, Sobotka said there would be a national debate on the country's place in the European Union in the case of British withdrawal from it.

[8] In December 2016, Sobotka called for higher corporate taxes, stating: "The way taxation is set up right now it only obliges the big and rich players, who export their profits out of the Czech Republic.