Mohammedan Sporting had appointed Sen as their new head coach for the remainder of the 2012/13 season. Sen's aim for the rest of the season was to gain promotion with Mohammedan Sporting to the I-League from the 2nd Division. He succeeded as the century-old side won the I-League 2nd Division, and earned promotion to the I-League 2013-14 along with Rangdajied. On 15 May 2013, he resigned as Mohammedan coach, he had revealed to The Telegraph that with his son Class X Board examinations approaching, it would be difficult for him to continue as the Mohammedan Sporting coach.
