In 1971, a group of Jesuits opened a middle school in the Lower East Side of Manhattan to serve the waves of Dominican and Puerto Rican immigrants settling in the area. The Nativity Mission Center provided their middle school-aged boys with an educational program in which they could excel academically, socially, and spiritually. The extended school day almost doubled that of the local public school, a low student-to-teacher ratio ensured time for one-on-one instruction, and a summer academic program extended learning year round. They made a commitment to support their graduates through high school and guide them on to college.

Ultimately, it became the inspiration for other educators seeking to provide outstanding education to urban students. More than 60 schools in 27 states operate today serving more than 4000 students.

In 2012, the provincial leaders of the religious congregations within the Diocese of Scranton endorsed an innovative educational project, involving collaboration among several religious congregations. The provincial leaders of interested congregations appointed a task force to investigate this idea and formulate a plan to meet the academic and social needs of low-income middle school children. Utilizing the successful Nativity School model and adapting it to meet the specific needs of the area, the vision for NativityMiguel School of Scranton was born.

No individual religious community had the resources to undertake such a project alone, so it became a collaborative effort among six religious congregations with long traditions of service to Scranton.