Maharjan made his national team debut on 25 March 2008 in a friendly match, in which Nepal won 1–0 against Pakistan in Pokhara, Kaski. On 31 August 2015, he won his 50th cap for
Nepal national football team in a friendly match against
India. He is the most capped player for Nepal national football team. He made his last appearance in Nepal jersey on 29 March 2021 at
Dasharath Rangasala, Kathmandu in which Nepal beat Bangladesh by 2 goal in finals of
Three Nations Cup. ==Honours==