The win helped Churchill Brothers take their points tally to 34 from 14 matches and enjoy a clear four-point lead at the top of the table with a match in hand against East Bengal, who are placed second with 30 points.
Roberto Mendes Da Silva scored the opening goal for Churchill Brothers in the fourth minute while a second-half penalty from Henri Arnaud made it 2-0 in the 71st minute.
American striker John Lada Matkin, making his debut for United Sikkim, pulled one back for the visitors in the 77th minute.
Churchill, who controlled the opening session, did not exert themselves and took the lead in the fourth minute through Roberto Mendes when he headed home a flag kick taken by Steven Dias.
Dias came up with two more good moves but Roberto's attempt was muffled and then Henri's header from close was saved by Sikkim goalkeeper Monotosh Ghosh.
In the second session, Churchill continued with their ball possession, but it was not until the 71st minute that they could add to their tally.
Denzil Franco made a fine run inside the Sikkim goal and was fouled by Safar Sardar, prompting the referee to point at the spot.
Henri stepped up and sent the goalkeeper the wrong way to make it 2-0.
Sikkim sensed a chance to take something out of the match when John Matkim scored after cutting past Israel Gurung and Lenny Rodrigues in the 77th minute.
The visitors tried to find the equaliser thereafter but Churchill's defence stood firm.