During the period of 2005–2010 he served as a presidential senior advisor for President Mahinda Rajapaksa and in 2007 he was appointed as a member of parliament from the national list.

He entered the parliament again from the national list and was appointed the Finance Minister during which he was accused of extreme negligence and mismanagement resulting in the worsening of the Sri Lankan economic crisis and was ultimately forced to resign under increasing protests by general public in the 2022 Sri Lankan political crisis.

His father, D. A. Rajapaksa, was a prominent politician, independence agitator, Member of Parliament and Cabinet Minister of Agriculture and Land in Wijeyananda Dahanayake's government.

[7] During his time as minister Sri Lanka had entered an economic crisis but Rajapaksa began avoiding parliament sessions for months.

[8][9] Other government MPs were also critical of his behaviour with Udaya Gammanpila, the energy minister claiming that Basil Rajapaksa refused to accept that an economic crisis was growing and that he knew nothing about his subject.

[10] Rajapakasa finally attended parliament on 5 April after an absence of four months and after being forced to resign after a series of protests against the government.

On 22 November he returned to Sri Lanka and despite not being an MP or holding any government position he was allowed to use the VIP lounge of Colombo Airport and was given a police escort.

[18] In 2016, the court ordered authorities to auction a luxury villa and 6.5 ha (16 acres) of land in Malwana, which is allegedly owned by Rajapaksa.

Financial Crimes Investigation Department (FCID), a police division that was established to punish the supporters of the previous government, filed charges against Rajapaksa.

[23] On 14 November 2023, following a case filed by filed by Transparency International Sri Lanka (TISL) and other four activists, the Supreme Court of Sri Lanka found Rajapaksa, his brothers Mahinda and Gotabaya and several other officials guilty of economic mismanagement between 2019 and 2022, and ordered them to pay about $450 (150,000 rupees) in legal costs to the petitioners.