[4] In November 2016, due to an injury to Dhanachandra Singh, which ruled the midfielder out for the rest of the season, Thapa joined the Chennaiyin squad as a replacement.

[5] He made his professional debut for the team on 1 December 2016, in his side's final match of the season against Goa.

[9] He made his first appearance of the season against Pune City on 3 December 2017, coming on as a 76th-minute substitute for Bikramjit Singh in a 1-0 win.

On 25 January 2018, he produced a man of the match performance against defending champions ATK for which he received great plaudits.

Former Chennaiyin head coach John Gregory even stated Thapa "as the next big thing in Indian football".

[10] He played in the final on 17 March 2018, against Bengaluru, coming on as a substitute as Chennaiyin won by the margin of 3-2, thus winning him his first league title.

He also made 8 appearances for the club in the 2019 AFC Cup, scoring a deflected goal against Abahani on 30 April 2019, but Chennaiyin failed to qualify from the group stage.

Thapa was the centre of their resurgence as he amassed 1 goal and 6 assists during the 2019–20 Indian Super League season.

Fortunately for the club, Thapa returned to full training ahead of its Indian Super League match against NorthEast United on 13 December 2020.