The place where the Mongar Lower Secondary School presently located was called Maantshang. In 1966, Thrimpon Karma, built the three storied building which served as a classroom from 1989 to 2003 as Mongar Primary School. There were classes from PP to IV. The first Headmaster was Mr. Lhundup Drukpa. The school gave its first PSLC exam in 1991. In 1998, the school was upgraded to a Junior High School and the school gave its first LSSCE (Class VIII) in 1999 with 95% pass result. The school moved to its new site on 27th March 2003.It has classes from PP to VIII with a total strength of almost 40 students in sections.