After the LionsXII was disbanded following the conclusion of the 2015 MSL season, Amri signed on a two-year contract with the Young Lions for the 2016 S.League season as one of three overage players, together with Firdaus Kasman and Christopher van Huizen. He was also named as the captain of the team. However, he was forced to miss out the opening weeks of the season due to an injury. Khairul only eventually made his first appearance in April, 5 months after his last competitive match. Khairul's injury ravage season saw him score only 5 goals all season.