To assess the effectiveness of intervention in improving knowledge, attitude and perception regarding smokeless tobacco (SLT) use and its harmful effects and intention to quit SLT among school going adolescents. A school-based cluster randomized control trial was carried out in 18 secondary schools targeting male and female students from grades 6 to 10 in Karachi. Primary outcome was knowledge about hazards of smokeless tobacco (SLT) and secondary outcomes were attitude and Perception about hazards of SLT, and intention to quit SLT. We enrolled 738 participants in intervention group and 589 in the control group. Mean score of knowledge significantly improved in intervention as compared to control group (P value \u3c 0.01). Intention to quit was found to be proportionately higher (33%) in the intervention group as compared to control group. Generalized estimating equations were used to assess the association of factors with knowledge regarding harmful effects of SLT use. Significant predictors of increase in knowledge score were found in children: who had seen any anti SLT messages on social media in the past 30 days, who were getting information regarding harmful effects of SLT use in school or textbooks and who had friends using SLT. A school-based intervention was effective in increasing knowledge regarding the harmful effects of SLT use and intention to quit SLT use among school adolescents. Introduction of such educational programmes on a regular basis in schools or as part of school curriculum can have an impact on reducing prevalence of SLT use.Trial Registration NCT03418506. https://register.clinicaltrials.gov/NCT03418506