Prajayatna started as a program of MAYA (Movement for Alternatives and Youth Awareness), which had been working since 1989 on the issue of child labour. Having spent its initial years campaigning against the issue, direct interventions with children and communities were initiated in the urban slums and low-income areas in Bangalore Urban and Rural districts. Enrolment of out-of-school children into non-formal education classes as preparation for enrolment into government schools was the focus. There was intensive work with parents to enhance their responsibility towards their children. Community-based structures like women's groups (Mahila sanghas) were initiated for involving parents in child care and were supported to address pertinent community issues and ensure that all children attend school.

The engagement with the education system, children and the community, over time, provided some critical and invaluable insights which significantly contributed towards initiation of Prajayatna. The strategy of re-enrolling drop-out children to school was found to be insufficient. It was learnt that it was the way the schooling system was designed that systematically alienated the children; that parents did not see the advantage of their children attending school the way it presently functioned nor did they see any role for them to engage with the school or affect its improvement. The situation of the school and what it offered provided little evidence of its functional advantage over other alternatives available to the parents and children.

The lack of accountability and transparency within the system and the complete absence of any form of control by the local community had resulted in very little consistent attention on their part to ensure that children remain in school and engage in any form of relevant learning. It was realized that little would change unless there is active participation of the community-parents, teachers, elected representatives, civil society groups, government functionaries and other concerned citizens – in educational reform, moving towards a situation where the community determines and manages the education system at the local level. Prajayatna thus evolved with a very clear goal of 'ensuring quality education to all children by facilitating community ownership of educational processes.'