JNV Aglar Shopian was inaugurated by His Excellency Sh. Jagmohan Malhotra, the then Honrable Governor of Jammu & Kashmir State in October 1986. The Vidyalaya was functioning in S.P. sheds up to December 1992 very smoothly, unfortunately the institution was set on blaze in the intervening night of 22nd & 23rd Dec 1992 by some miscreants. The district level administration shifted the Vidyalaya to Awantipora, Distt. Pulwama in rented buildings. The Vidyalaya was functioning there up to December 2003. The NVS authorities got the gutted S.P. sheds renovated and shifted back the institution to its permanent site in the village Aglar in March 2003. Since March 2003 the Vidyalaya is running smoothly in the same renovated S.P. Sheds till date. For the permanent construction of the Vidyalaya buildings the NVS Noida authorities have allotted the construction work to JKPCC and the said agency has started to execute the work in 2007 but unfortunately the construction work of Phase 'A' is still incomplete. However, the Academic Block, one Boys Hostel and one Girls Hostel have been taken over the the Vidyalaya from the said agency just before the beginning of academic session 2022-23.

Today, JNV Shopian is swiftly moving towards the best phase with regards to infrastructural development as the Phase 'B' work is also under process. The school prides itself of having a strong workforce and bright students. It has been equipped with sports equipment, smart lab, computer lab, smart classroom, tablets and internet connectivity for its students. The school administration has been upgraded with the help of administrative staff, modern machinery like computers, laptops, printers, zerox machine, etc along with fast internet connectivity.