This study investigates the enjoyment and cohesion of school children participating in a school-based high-intensity physical activity (PA) intervention. Both enjoyment and cohesion have been found to be important factors for adherence to regular physical and sport activity, an important outcome of PA interventions. The sample consisted of 300 pupils (mean age: 9.3 years; 52.7% female) assigned to a team sport intervention, an individual sport intervention, or a control group for 10 months. The Physical Activity Enjoyment Scale and Youth Sport Environment Questionnaire were used to measure enjoyment and cohesion. The Yo-Yo IR1C test determined fitness improvements. Results showed that enjoyment and cohesion (social) measured at the beginning of the intervention significantly predict fitness improvements achieved after 10 months. No differing developmental effects over time could be found in the intervention groups with regard to cohesion and enjoyment when comparing them to the control group. However, enjoyment and cohesion (social) significantly decreased in the groups that performed individual sports. Team sports seem to be more advantageous for the development of enjoyment and cohesion, which are both factors that positively impact the health outcomes of the intervention.