Supplier: Shiv Naresh / Sponsors: Legion On 14 June 2016 Mohun Bagan announced that they would be fielding a junior side in the Calcutta Football League which would be mentored by assistant coach Sankarlal Chakraborty.
The club officials also announced that they would not be fielding a side in the exhibition matches of the Calcutta Football League against East Bengal and Mohammedan due to disagreement with the IFA over television broadcast rights sharing and match-day ticket distribution.
The Mariners got off to a brilliant start in the season as they demolished their opponents 5–1, courtesy a hat-trick from Darryl Duffy and goals each from Prabir Das and Azharuddin Mallick.
On 16 August 2016, Mohun Bagan announced the signing of Haroon Fakruddin in place of English defender Danny Seaborne who left the club on basis of a mutual understanding.
[5] On 17 August 2016, Mohun Bagan announced the signing of their third foreigner for the Calcutta football league as they finalised a deal with Nigerian striker Daniel Bedemi.
[35] On 2 September 2016, Mohun Bagan finally returned to winning ways, when they defeated United 3–1 courtesy a brace from Daniel Bedemi and a solitary goal from Darryl Duffy.
On 7 Sepeteber 2016, Mohun Bagan refused to take the field in the scheduled Kolkata Derby and gave arch-rivals East Bengal a walkover, citing lack of opportunities of pre-match practice at the Kalyani Stadium.
Mohun Bagan continued their winning run into the 2nd match of the league, when they defeated Shillong Lajong 2–0 at home, owing to a brace from Scottish striker Darryl Duffy.
The Mariners bulldozed league newcomers Minerva Punjab by a 4–0 margin, as star player, Sony Norde made his first appearance of the season.
Mohun Bagan continued their winning run in the season for the 4th consecutive match when they edged past newcomers Chennai City 2–1 in an away encounter with goals from Jeje Lalpekhlua and Sony Norde.
Mohun Bagan played out their first draw against DSK Shivajians in the 5th round of the league, with the scoreline remaining at 0–0 post 90 minutes, owing to a lackluster performance from the Green and Maroon strike force.
Mohun Bagan returned to winning ways as they got their AFC Cup campaign running with a 2–1 away victory over Sri Lankan side Colombo, with Kean Lewis and Sehnaj Singh finding the back of the net for the Mariners.
Mohun Bagan continued their winning run in the AFC Cup as they defeated Colombo 2–1 in the home leg encounter at the Rabindra Sarobar Stadium.
Mohun Bagan finally returned to winning ways in their next match at home against DSK Shivajians when they defeated the latter 3–1 courtesy a brace from Balwant Singh, while Katsumi Yusa netted his first of the season from the spot.
Mohun Bagan failed to return to winning ways in their home encounter against Mumbai where they played out a 2–2 draw courtesy goals from Pritam Kotal and Balwant Singh.
The Mariners were up against Bengaluru FC in an I-League away encounter next, where they played out a respectable goalless draw after being brought down to 10 men, courtesy a double yellow card to Subhasish Bose.
In the 2nd half, East Bengal made the job even more difficult for themselves as Willis Plaza was given the marching orders by the referee for an off the ball push on Anas Edathodika.