Born in Tuibuong, Manipur, Khongsai moved to Delhi in 2014 due to the violence and economic hardship.[1] In 2017, Khongsai joined the youth academy at Sudeva. In 2019, he went to Spain and joined Tercera División side Olímpic de Xàtiva, which is affiliated with Sudeva Delhi.[1][2]
On 9 January 2021, Khongsai made his professional debut for Sudeva Delhi in their opening I-League match against Mohammedan. He started and played 71 minutes as Sudeva were defeated 0–1.[3]
In 2022–23 season, Sudeva Delhi got relegated from I-League.[4][5]