​In 1970, eleven acres of property at the end of Marilyn Avenue was purchased for $22,500. for a proposed school and a Catholic school zone was established for the Town of Napanee and area. In November 1976, a survey indicated that 89 children might attend this Catholic school. The Frontenac-Lennox and Addington County Roman Catholic Separate School Board decided to proceed with a temporary building. The temporary portable school, called Napanee Separate School, was opened in the fall of 1977, with four classrooms, 104 students, four teachers, a part-time secretary and a part-time custodian. The school's first principal Joe Hamilton.

Rev. John Joseph O'Neill, became pastor of St. Patrick's Church in Napanee in 1969. Father O'Neill was instrumental in the purchase of the land for the school. He was the driving force in the community, parish, and school. In 1978, Napanee Separate School was renamed "J.J. O'Neill Catholic School" in honour of the pastor of St. Patrick's Parish, Napanee.

In March 1982, an allocation of funds was approved for the core unit of the permanent school. The architectural firm of Jackson-Ypes was chosen by the Board and prepared sketch plans. By April of 1983, the firm of M. Sullivan & Son began construction to the new school. With the completion of construction in January 1984, the school had expanded to seven classrooms, 203 students, 11 teachers, a part-time secretary and a full time custodian. The official opening and blessing of the school was held on June 17, 1984.

J.J. O'Neill Catholic School, has continued to expand over the years in terms of physical space, yard enhancements, programme, staff and student population. In the school year of 2017-2018, there were 289 students and a staff of over 30.

The School Council is an active one, working very hard to improve student learning. One major accomplishment was the work involved to raise funds for a primary playground installed in September 1999. 

J.J. O'Neill Catholic School is proud to promote academic excellence, and a strong athletic tradition in its sports teams. A student council plans social events such as pizza days, dances, Spirit Week and playdays.

J.J. O'Neill has hard working and committed staff that share a common faith. They are committed to providing each student the opportunity to grow in faith, respect and concern for each other, while at the same time developing spiritual, academic, physical and social potential in our young people.