Background Behavioural risk factors are often present during adolescence and account for 70% of premature deaths during adulthood. Excessive sedentary behaviour and screen time have become significant concerns, especially among adolescents, due to their potential negative impact on physical and mental health. Adolescents with a high screen-based sedentary time are more likely to be physically inactive, have unhealthy body structure and poor academic performance. The objective of our study is to assess the effect of multi-component modular educational intervention on screen-based sedentary time (SST) and non-screen-based Sedentary time (NSST) among adolescents. Methods Ethical approval for the study has been obtained from the institutional Ethics Committee of Kasturba Medical College in Mangalore, India. This cluster randomized control trial will be carried out in schools located in the urban area of Mangalore. Using simple randomization, the eligible schools will be randomized into intervention and control arms, each consisting of 10 clusters. A multi-component modular educational intervention will be administered to participants in the intervention group at baseline, second and fourth month. The control group will receive the standard curriculum. Both the groups will be assessed at baseline and at second month, fourth month and sixth month of follow up for SST, NSST and level of physical activity. Anthropometric measurements like height, weight, waist circumference and hip circumference will be taken at baseline and sixth month of follow up. Results A comprehensive school-based modular educational intervention can have cumulative advantages by reducing screen- and non-screen-based sedentary time, and encouraging physical activity. Similar modular teaching can be incorporated into the curriculum, which will promote healthy life-style among the adolescents.