Introduction: Rates of primary school enrolment have improved in India, but levels of learning achievement remain low. In the Support To Rural India’s Public Education System (STRIPES) trial, a para-instructor intervention improved numeracy and literacy levels in Telangana, India (2008−10). The STRIPES2 trial was designed to assess whether a similar intervention in a younger cohort of children would have similar effects in Satna and Maihar districts of Madhya Pradesh, India, and be cost-effective. Methods: In this Madhya Pradesh cluster-randomized controlled trial, 196 villages (clusters) were randomized to receive either a health (CHAMPION2: community health promotion and medical provision and impact on neonates) or education (STRIPES2) intervention. Villages receiving the health intervention were controls for the education intervention and vice versa . For children newly enrolled in primary school, the STRIPES2 intervention comprised before/after-school classes (2 hours per day, 6 days a week) given by trained para-instructors from the local community, frequent monitoring, and engagement with caregivers to motivate children, delivered by the Pratham Education Foundation. STRIPES2 activities had to be suspended twice for around ten and a half months, and some components of the intervention modified due to the COVID-19 pandemic. The period of the trial was extended with the primary outcome (a composite literacy and numeracy score of Early Grade Reading and Mathematics Assessments) assessed around 30 months after classes started. Results: Composite test scores were significantly higher in the intervention arm (98 villages; 3054 children) than in the control arm (98 villages; 3275 children) at the end of the trial. The mean difference on a percentage point scale was 14.17; 95% CI 11.36 to 16.97; p < 0.001, equating to a 0.58 (95% CI 0.47 to 0.71) standard deviation difference. The cost per child per 0.1 SD increase in composite test score was INR 2476 (US$33.5). Conclusion: Despite COVID-19 interruptions and disruptions, STRIPES2 resulted in a major improvement in children’s literacy and numeracy. However, the cost of achieving such benefits was substantial.