Boyko was deputy Minister of Fuel and Energy in the cabinet of Viktor Yanukovych (21 November 2002 – 7 December 2004). Late July 2004 he was appointed in a coordination committee for RosUkrEnergo. On April 23, 2005 Boyko was elected the Chairman of the Republican Party of Ukraine (RPU). During Ukrainian parliamentary elections in 2006, the RPU joined the Opposition Bloc “Ne Tak!”, yet they did not succeed to reach the 3% election threshold required by law. In the summer of 2005 President Viktor Yushchenko prevented Boyko to be arrested for abuse of office while heading Naftogaz. This arrest had been ordered by Security Service of Ukraine Chairman Oleksandr Turchynov. On 4 August 2006, he was appointed the Minister of Fuel and Energy (in the government of Viktor Yanukovych). On 18 December 2007 Boyko was dismissed as Minister of Fuel and Energy of Ukraine due to the election to the 6th parliamentary elections.
November 2007 – March 2010 – People’s Deputy of Ukraine, the 6th convocation of Verkhovna Rada, elected from the Party of Regions in the Ukrainian parliamentary elections in 2007.
On 11 March 2010 Boyko was appointed the Minister of Fuel and Energy of Ukraine (in Mykola Azarov government)
On 9 December 2010, due to the optimization of the system of central executive power in Ukraine (a.k.a. reorganization of ministries) President of Ukraine V. Yanukovych dismissed Boyko from the position of Minister of Fuel and Energy of Ukraine and appointed him the Minister of Energy and Coal Industry of Ukraine.
According to a left-leaning newspaper “Dzerkalo Tyzhnia” (“The Weekly Mirror”), in 2011 Yuriy Boyko was cited confirming the purchase of a modern offshore drilling platform from Singapore. Dzerkalo Tyzhnia conduct and investigation into the tender surrounding the offshore platform, which HIGHWAY INVESTMENT PROCESSING LLC, a supposed offshore shell from Wales, UK was the winner. The article stated that the Ukrainian State company Chornomornaftogaz, engaged in offshore oil and gas production in Azov and Black Sea, paid over $400M for a drilling rig that costs $248M (suggested manufacturer price). Using Google Street View, journalists cited that HIGHWAY INVESTMENT PROCESSING LLC appears to be situated in an equipment store on the outskirts of Cardiff, Wales. HIGHWAY INVESTMENTS LLC was further cited in the media as going through liquidation, however, the authorities suspended the liquidation process due to an investigation. Official records with United Kingdoms Companies House indicate the company was incorporate on 12 December 2008 and is currently listed as active. Throughout the whole affair, Yuriy Boyko denied fraud allegations surrounding the purchase, citing additional equipment and movement costs and a “report from Halliburton” confirming the price of $400M. Boyko labeled the “Dzerkalo Tyzhnia” journalists as “liars,” “Dzerkalo Tyzhnia” in turn filed a lawsuit against Mr. Boyko which the Ukrainian court did not accept and the case is currently in appeals. Meanwhile, the affair has sparked a scandal in Norway where Seadrill was accused of insufficient due diligence and KYC on its shell customer HIGHWAY INVESTMENT PROCESSING LLC.
On December 24, 2012 Boiko was appointed a Vice Prime Minister in sphere of ecology, natural resources, energy, coal industry and industrial policy. On 23 May 2013 the space sector was added to his functions.