Samdrup Jongkhar Higher 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 7.421 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 populations 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. The school was further upgraded to Higher Secondary School in the year 2022 under the leadership of Principal master Kesang Tshering.
This is the only Higher Secondary School, which is within the vicinity of the Thromde and Dzongkhag Headquarter. The school is well staffed and sound in infrastructural facilities. 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(s)/Principal is:
| Sl.# | Year | Name | Type of school |
| 1 | 1984-1986 | Mrs. Chhetri | Primary School |
| 2 | 1987 | Mr. Gopi Nathan | Primary School |
| 3 | 1988 | Mr. TsongponWangdi | Primary School |
| 4 | 1989 | Lop. Kuenzang | Primary School |
| 5 | 1990-1993 | Mr. NimaGyeltshen | Primary School |
| 6 | 1994-1995 | Mr. Karma Wangchuk | Primary School |
| 7 | 1996-1999 | Mr. Dawa Tshering | Junior School |
| 8 | 2000-2006 | Mrs K.C.Dorji | Middle S. School |
| 9 | 2007-2017 | Mr Norbu | Middle S. School |
| 10 | 2018-2021 | Mr. Kesang Tshering | Middle S. School |
| 11 | 2022- | Mr. Kesang Tshering | Higher S. School |