Bagan are already out of AFC Cup while Bengaluru as the group E toppers have already qualified for the next stage.
However the crazy scheduling of Federation Cup meant that the final is being played a week after the semi-finals with the second tier continental championship sandwiched in between.
This will be their fifth meeting this season, with the first of those matches took place in Bengaluru on March 11.
They will meet again for the sixth time on May 21 in Cuttack in the Federation Cup final that will also give the winners an AFC Cup slot for the 2018 season.
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On nine points from four matches to lead the table, Bengaluru will look to log full points to secure their passage to knock-out stage.
The third-placed Mohun Bagan who have three points from four matches will look to finish on a high at their home venue where they have been unbeaten this season.
Mohun Bagan lost 2-5 to Maziya Sports and Recreation of Maldives at the National Stadium in Male on May 3.
Bengaluru FC went down 0-2 to Abahani Limited Dhaka at the Bangabandhu National Stadium in Dhaka on the same day.
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