Shilton D'Silva headed home the opener in the 18th minute but an own-goal by Lalchhawnkima (21') and a good finish by Marcus Joseph (24') put the visitors in the driving seat. Aser Dipanda scored at the hour-mark to rescue a point for the hosts.
Khalid Jamil made three alterations to the side that went down in the Kolkata Derby. Arijit Bagui, Azharuddin Mallick and Shilton DSilva got the nod ahead of Abhishek Ambekar, Pintu Mahata and Darren Caldeira respectively.
Gift Raikhan made four changes to the starting XI that earned a point against Minerva Punjab in their last match. New recruit Fabien Vorbe got a start along with Mohamed Irshad, Bijesh Balan, and Suhair VP.
Gokulam could have gone ahead in the very first minute when Marcus Joseph fired a shot from distance and Shilton Paul, who was caught off his line, stumbled while tracking back. Luck favoured Bagan as his shot missed the target by a whisker.
Gokulam maintained their ascendency as they continuously out-manoeuvred Bagan's midfield.
It took some time for the hosts to get a foot-hold of the match and they drew first blood on the 18th minute when Sony Norde delivered a curler from a flag-kick and Shilton D'Silva nodded it home.
But Gokulam got back in no time as Lalchhawnkima's misplaced clearance of a Bijesh Balan cross nestled at the back of the net.
Three minutes later Joseph fired his team into the lead after he latched on to a pass from Suhair VP in the attacking third and chipped over Paul to score his third goal in as many matches. Eze Kingsley was once again found wanting as he reacted late to Joseph's run and could not recover in time.
Minutes before the end of first-half, Dipanda missed a header from six yards despite being completely unmarked.
Bagan started to show some urgency in the second half but were struggling to make forays into the attacking third. Omar had a forgettable day in the office as he was tightly marked by Fabien Vorbe.
Bagan did equalise on the hour-mark when Dipanda finally found the net after he got his head to a lobbed ball by Kisekka from the edge of the box.
The introduction of Mehtab Hossain added some steel into the midfield for Bagan but their lack of cutting edge in the attacking third did not help in their search for the winner.