Samdrup Jongkhar Middle Secondary School was established in 1984. It is located in an ideal place where teaching and learning takes place smoothly. It is very near to the hospital and away from the hustle and bustle of the market area. Flowering plants and trees of different types cover the area of 7.04 acres of land.
When it was first incepted, it offered primary level education to the students. Gradually, to provide better education services to the growing number of population the school was up-graded to Junior School in 1996 offering classes from PP to VIII. In the year 2000, the School was up-graded to Middle Secondary School under the Headship of Mrs. K.C. Dorji. This is the only Middle Secondary School, which is within the vicinity of the Dzongkhag Headquarter. Due to this, the school is facing admission pressure every year from all sections of the population. Yet, the school is well staffed and sound in infrastructural facility. Therefore, it could provide ever increasing needs of the society for their children�s education. As per the school profile, the school went under different Heads since 1984. The chronological order of the Head Teacher is:

Sl.no. Name Year Types of school
1 Mrs Chhetri 1984-1986 Primary School
2 Mr Gopi Nathan 1987 Primary School
3 Mr Tshongpon Wangdi 1988 Primary School
4 Lop Kuenzang 1989 Primary School
5 Mr Nima Gyeltshen 1990-1993 Primary School
6 Mr Karma Wangchuk 1994-1995 Primary School
7 Mr Dawa Tshering 1996-1999 Lower Secondary School
8 Mrs K.C.Dorji 2000-2006 Middle Secondary School
9 Mr Norbu 2007-2017 Middle Secondary School
10 Mr Kezang Tshering 2018-Till Date Middle Secondary School