Purpose: The primary goal of this study was to investigate the association between physical activity and school achievement in adolescents and adolescents in the context of the degree of their general nutrition and abdominal nutrition. Methods: The sample was consisted of 831 high school students from the city of Zagreb (425 boys and 406 girls with an average age of 15.5 ± 0.2 years) who were randomly selected and longitudinally monitored as part of the CRO-PALS study. Based on the morphological characteristics, including body height, weight and waist circumference collected in the first year of the project, 2014/15 school year, the respondents for the purposes of this paper are classified according to four categories of body mass index into groups malnutrition, normal nutrition, overweight and obesity, and additionally in two categories according to the limit values of normal waist circumference in the groups normal waist circumference and abdominal obesity. Data on the level of physical activity of students were collected and assessed using the SHAPES questionnaire based on recollection of physical activity and its intensity during the previous seven days, and data on overall school success and final grade in mathematics by supplementing the questionnaire at the end of the school year. The variables that were observed and correlated with each other were: level of physical activity, school success, level of nutrition and abdominal obesity. Results: Analysis of the results in already formed groups showed that there are no significant positive or negative associations between different physical activities and school success, ie., higher levels of physical activity are not accompanied by achieving better school achievement. A negative association of physical activity with the final grade in mathematics was observed in a relatively small group of abdominal obese girls. Conclusion: From the results of this work, it seems that increasing the level of physical activity does not negatively or positively affect school achievement, regardless of the level of nutrition of adolescents. Given the positive effects of physical activity on the mental and physical health of adolescents identified by previous researches, city policies should promote an increase in physical activity in adolescents, with particular emphasis on the overweights. Additional researches are needed to prove the positive effects of physical activity on adolescents ’school achievement.