Navodaya Institution was established in the year 2005 exclusively for the education and skill development of the children of the Chepang Indigenous Community of Nepal. It has been founded by Nepal Little Flower Society of the Little Flower Province of the CST Fathers in the Vicariate of Nepal. The vulnerable nature of the Chepang Community and its lack of opportunity for education and development have motivated the Little Flower Society to establish this institution with a school and a hostel for these children, and to engage itself in developmental programs focusing on the Chepang settlements. Fr. Michael Chirayath CST has been appointed in-charge of the institution. .

From the year 2005 April to 2011 October the school and hostel were run on rent in the building owned by Mr. Kamalchand Khanal at Jayamangala, Ratnanagar-13, Chitwan District. Mrs Sunimaya Chepang was the first Principal of the school. Bro. Gijo Panthackal CST and Mrs Sarswati Mainali looked after the children in the first year. In the year 2006 Bro. Gijo left the place for his higher studies, and in the same year in July the Sisters of Charity of Maria Bambina (SCCG) joined the institution to render their services. Sr. Jiliola D’Souza and Sr.Hilda Lewis were the first two Sisters who came to help in the activities of the institution and Sr. Regina Lonappan joined them later. Sr. Jiliola was appointed Principal of the school in July 2006.

In the year 2008 December 45 khatas of land was bought at Tharkari Chowk, Chainpur-1, and in 2009 January 21 khatas of adjacent land also was bought to establish the school and hostel. In November 2009 SCCG Sisters too bought nearly 12 khatas of land attached to the existing land.

Sr. Evelyn Varkey was appointed Principal of the School and Superior of the Convent in July 2009.

MISSO Munchen generously came forward to support the school buildings and hostels with financial assistance by WITRON Foundation, Germany. In February 2010 the construction of the school building was started and was completed in November 2011. The new School building was blessed by Bishop Antony Sharma on 12 November 2011 and was inaugurated by Mr. Kamal Pokharel, Joint Director, Department of Education, on the same day followed by cultural programs staged by the children. The convent building also was blessed by the Bishop on the same day.

The new building for the Girls’ Hostel, supported by MISSIO, was completed in July 2013 and girls started staying in it. Construction work of all the buildings was supervised by Fr. Cherian Elavakunnel CST.

The foundation stone for the Boys’ Hostel was blessed by Fr. Sebastian Thundathil CST on 18 February 2014, and was laid by Mrs Branka Begic from MISSIO Germany. It was inaugurated on 28 February 2015 by Tobias Winkler and Bernhard Solfrank.

The first batch of the school appeared for the SLC exam in the year 2014 and out of 20 one failed. In the second batch (year 2015) out of 20 only eleven passed.

The school was recognized up to the Secondary Level by the Department of Education in 2013, and Class X was approved in 11 April 2014.