(1) Introduction: Regular physical activity (PA) is an important part of a healthy lifestyle for children and adolescents. The aim of this study was to assess the impact of an increase in organized PA at school on the physical fitness (PF) of early adolescent boys and girls. (2) Methods: A total of 294 children born in 2007 took part in the study. The sample was divided into two groups: of increased PA at school (n = 140, girls n = 66, boys n = 74) and standard PA (n = 154, girls G n = 70, boys n = 84). Increased and standard PA levels consisted of 10 and 4 h of physical education lessons (PE) per week, respectively. PE consisted of team games and fitness exercises. Three of the Eurofit tests, core strength, long jump, and running speed, were used to measure PF. Tests were conducted in May 2018 and 2019, at an average age of a participant of 11 and 12 years, respectively. Descriptive statistics and cluster analysis were applied for analyzing the results. (3) Results: After one year of observation PF of children was improved in both groups (p < 0.001). However, it was greater in the increased PA group than in the standard one. A higher percentage of very good scores and lower of poor and very poor were noted in the increased PA group than the standard one (20.36% vs. 12.90%, p = 0.003 and 18.58% vs. 24.85%, p = 0.022, respectively). Boys obtained better results than girls (p = 0.003). Children achieved the best results in the shuttle run test, and the worst in the core strength. Children with normal body mass obtained better results than those with excessive ones. (4) Conclusions: Increasing the number of PE at school beneficially affects the fitness performance of early adolescents. To improve the health status of adolescents it is advisable to increase the number of compulsory PE lessons in the school curriculum.