KJP Synod Sepngi Higher Secondary School, formerly known as Christian High School, came into existence after the foundation of the Adhoc Managing Committee on the 13th of June 1981. The committee included Tbn. T. Roy Lyngdoh (president), Mr. A. Dkhar (secretary), Tbn. B.D Dkhar (treasurer), and other members.

The School was established on the 15th February 1982 by the New Nongstoin District Presbyterian Church, bearing the name Christian Secondary School under Rev. B.C. Lyngdoh as the honorary headmaster. In 2006, the school was handed over to the Khasi Jaintia Presbyterian Synod Sepngi as the managing body, which rechristened the school to KJP Synod Sepngi Higher Secondary School, Nongstoin.

The School was registered under the Recognition/Opening permission which was recognized by MBOSE, Memo No. MBOSE/TS/Recog/Voll-III/87/2135-4/Dt. Tura 22nd February 1989. The School is also recognized by the government of Meghalaya vide memo letter No. DSEL/SEC-NG/Recog/1/2012/36 'A', Dt.5.8.2012.

The School was registered under the registering Act of Society Act 1880 under the Khasi Jaintia Presbyterian Synod Sepngi, Church House, Mission Compound Shillong-2 Meghalaya, which is also the sponsoring body.