Rahul was ruled out of the first test in Galle, where India won by 304 runs, with a viral fever but the 25-year-old has recovered sufficiently and has been batting in the nets.
"KL has been our established opener. I feel one of the openers (from the first test) has to make way," Kohli told reporters in Colombo on the eve of Thursday's match at the Sinhalese Sports Club Ground.
"What he has done for us in the past two years has been very solid and he deserves to come back in and start fresh in test cricket again.
"We have a team meeting later on after practise, so we will be able to clarify that then but yes KL, according to me, will definitely come back."
India were without both their first choice openers in Galle, with Murali Vijay also unavailable due to injury.
Shikhar Dhawan, who was named in the squad as a replacement for Vijay, and Mukund opened for the tourists, who eased to a 1-0 lead in the three-test series.
While Dhawan put India in the driver's seat on the opening day with a sparkling 190 off just 168 deliveries, it was Mukund's turn to shine in the second innings with an 81.
"In a situation like this you need to sit down and think which player has had more impact on the game and who's been able to make that difference in the game straight away," Kohli said, hinting that Dhawan will get the nod.
"It all depends on who's had a better game. Honestly, it's a very thin line, it's a very small margin but unfortunately that's how this sport goes sometimes."
Rahul had been due to return to the Indian starting lineup after recovering from a shoulder injury sustained during the home test series against Australia.
The right-handed batsman has scored four hundreds and seven fifties in 17 tests with a top score of 199.
"It's very important to make him feel that this is his spot," Kohli said. "It won't be changed because of unfortunate events that happen outside the playing field or the injuries that you can't control.
"That phase you have to come back, get stronger... he's really stuck it out in that phase. It's been hard for him, he was batting very well and then he had to be out.
"It's very important to make him feel secure and he deserves it because he's given us those big performances when the team has required them. So he's a guy who needs to be back, we... all back him."
(Reporting by Sudipto Ganguly in Mumbai; Editing by John O'Brien)
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