The research was conducted to measure the effect of health literacy-grounded web-based education program on health literacy, nutrition and exercise behaviours in adolescents. The increasing prevalence of obesity in adolescents is explained by a sedentary lifestyle and unhealthy diet. Health literacy is essential for adolescents to maintain their healthy behaviours. The research was conducted as a parallel group randomized controlled trial. The study was completed by 114 adolescents (experimental = 42, control = 72). The Personal Information Form, the Health Literacy Scale for School-Age Children and the Nutrition and Exercise Subscales were used to collect data. A web-based education program was implemented. Two-way mixed design ANOVA with Bonferroni test was used to examine the group, time and group*time interaction of the measurements. There was no statistically significant difference between the experimental and control groups regarding health literacy level, nutrition and exercise behaviours pre-test mean scores (p > 0.05). In the post-test, the mean scores of health literacy and nutrition behaviours in the experimental group were higher than the control group (p < 0.001). However, there was no significant difference in exercise behaviours (p > 0.05). The power and effect size in mean scores changes for health literacy (99.8%, η2 = 0.039) and nutrition (99.8%, η2 = 0.039) were moderate. The study concluded that health literacy-grounded web-based education program increased the health literacy levels of adolescents and improved their nutritional behaviours; however, there was no sufficient change in exercise behaviours.