The accused, identified as Ram Prasad Adhikari, was remanded to judicial custody for 10 days after he was produced at Chitwan District Court.
Police are also looking for 10 other accused in the case.
Ram Prasad was arrested on Friday for the murder of Krishna Prasad Adhikari in 2004.
Krishna's agitating parents, Nanda Prasad and Ganga Maya Adhikari of Gorkha district, who were on a fast-unto-death since the last 47 days demanding action against Maoist cadres involved in the murder of their son, finally ended their fast late last night.
Maoist leaders, including UCPN-Maoist chief Prachanda, had warned the government against taking any action against their cadres, saying that war-time crimes could not be put on trial.
The Nepalese Civil War fought between government forces and Maoist fighters lasted from 1996 until 2006, killing thousands.
