cientific Initiation (SI) in high school has increasingly been recognized as a relevant pedagogical strategy for fostering critical thinking, intellectual autonomy, and student protagonism. Within the context of the Full-Time School Program (PEI) of the State of São Paulo, school-based research plays an important role in students’ comprehensive education, promoting the integration of theoretical knowledge and investigative practices. This study aimed to analyze the contribution of scientific initiation to scientific literacy and youth protagonism through an experimental investigation of the antioxidant activity of the Noni fruit (Morinda citrifolia L.). The research was conducted in a public school in the state of São Paulo, within Experimental Practices classes, using an action-research approach and an investigative methodology. Students carried out a literature review, sample collection, extract preparation, and qualitative phytochemical tests to identify secondary metabolites, as well as an evaluation of antioxidant activity using the DPPH free radical method. The results indicated the presence of phenolic compounds, flavonoids, alkaloids, anthraquinones, saponins, tannins, and terpenes/steroids, in addition to evidence of moderate antioxidant activity. From a pedagogical perspective, high student engagement was observed during the activities, contributing to the development of scientific skills such as observation, data recording, result interpretation, and scientific argumentation. It is concluded that scientific initiation within the PEI context contributes to scientific literacy and to the development of more critical and autonomous students.