[citation needed] After the dissolution of Parliament and declaration of emergency by King Gyanendra, Thapa took a vehement stand against the royal regime and called for the establishment of a republic.

[11][12] Following a Special Court order in July 2005, Thapa was arrested from the Singha Durbar Ward Police Station where he had gone to meet his colleagues,[13] and was subsequently interrogated by The Office of the Kathmandu District Government Attorney for his involvement in 'offense against the state' by chanting anti-monarchy slogans at a rally.

Thapa was excluded from the race by Nepal Congress Party President, Girija Prasad Koirala, on charges of being 'agents of the palace' alongside NC Central Member Narhari Acharya.

[20][21][22][23][24] During the 12th National Convention of the NSU in 2007, Thapa pulled out his candidacy for the post of President, claiming that "The NC leadership has remained biased against me and therefore I have declared that I would not contest".

[25] Gagan Thapa was elected to the First Constituent Assembly (CA) under the party-list proportional representation system from Nepali Congress.

[26] Thapa won a seat in the Central Working Committee of Nepali Congress in the 12th National Convention held in 2010, receiving the highest number of votes.

[39] Thapa was critical of the Information Technology Bill on grounds of it "curtailing the fundamental rights of people to freedom of expression and opinion, and was hence against the spirit of the constitution.

"[40][41] On 29 November 2018, Thapa had called for a civil disobedience against the 4 day odd-even traffic rule issued to manage the Asia Pacific Summit 2018 by the government.

Thapa commented that the organization had a controversial history of accusations of mass proselytism as well as the illegal promotion of Christianity and the public should not suffer for such an unjust cause.

[42] In March 2016, Thapa unsuccessfully contested for the post of the Nepali Congress Party's general secretary, competing against Arjun Narsingh KC (his father-in-law), and Shashank Koirala.

[45] As a Central Committee Member,[46] Thapa has called for a change in the Nepali Congress's leadership through a special party convention.