Khogen started out his football career as a player turning up for Air India FC, Salgaocar FC and Mumbai FC among others. His first prominent managerial role was with I-League newcomers Minerva Punjab in 2017-18 and he helped them win the league in only their second season in the top flight. He left the club after he was offered a youth coaching role the following season.
The Manipuri will be taking over the Imphal-based NEROCA FC for the upcoming I-League season. NEROCA FC finished bottom of the table last season, but were not relegated as the AIFF decided to reinstate the team owing to the COVID-19 pandemic.