Objective: To identify physical fitness and activity levels, and health-related quality of life of children with epilepsy in Turkey and compare the results with their healthy peers. Methods: The study included 21 children with epilepsy (with no seizures and not taking anti-epileptic drugs for at least a year) and 20 healthy peers. The FitnessGram Physical Fitness Test Battery was used to assess physical fitness, the 6-Minute Walk Test to assess physical performance, the Pediatric Quality of Life Inventory 4.0 (PedsQL) to assess the quality of life, and a pedometer was used to assess the physical activity of the children. Results: The physical fitness assessments including the trunk-lift test and flamingo balance test results were significantly lower in the children with epilepsy (p < 0.05). There was no significant difference between the groups in terms of BMI, the cadence-based curl-up test, the push-up test and the back saver sit/reach test (p > 0.05). Physical activity, physical performance, and quality of life results were significantly lower in children with epilepsy (p < 0.05). Conclusion: The presence of epilepsy may negatively affect many aspects of physical fitness, physical activity, and quality of life in childhood. The children with epilepsy adopted a more sedentary lifestyle than their healthy peers. Quality of life outcomes reveal that epilepsy has negative physical and psychosocial effects on children. These results support the necessity of raising awareness in both health professionals and families to encourage their children to be more active.