This study assesses the effects of an educational gamification program on motivation, engagement, and flow for high school students from socially disadvantaged communities. A quantitative comparison was carried out with pretest--post-test measurements with intervention and control groups. A total of 216 students from two high schools in socially deprived areas participated in the study. The experimental group engaged with a gamified platform for seven 1 h sessions while the control group continued their directive lessons. The results indicate that the experimental group significantly improved its flow, engagement, and motivation score compared to the control group. We concluded by highlighting the usefulness of gamification to motivate socially deprived students in learning scientific subjects.