The first leg will be held at the Changlimithan Stadium in Thimpu on January 23.
The return leg will be organised at the Kanteerava Stadium on January 30.
The ISL franchise qualified for the 2018 AFC Cup by virtue of being the Federation Cup champions.
Bengaluru FC had a good run in the 2016 edition, finishing as runners-up after losing to Iraq's Air Force Club.
In this year's edition, they went down 2-3 on aggregate to FC Istiklol in the AFC Cup Inter-Zonal Final.