Objective This study aimed to analyze the current status and influencing factors of physical activity in children with epilepsy, providing evidence for developing targeted intervention strategies. Methods A cross-sectional survey was conducted from July 2024 to March 2025, involving 97 children with epilepsy aged 6 ~ 19 years with undergoing 24-hour electroencephalogram monitoring and parents of pediatric patients from a tertiary hospital in Shandong Province, China. The General Information Questionnaire, the Physical Activity Intention Scale for Children and Adolescents with Cancer, the Godin Leisure Time Physical Activity Questionnaire, and Tampa Scale for Kinesiophobia-11 were used to investigate general information about children and adolescents with epilepsy and parents, attitudes, perceived behavioral control, and behavioral intentions, the physical activity, and kinesiophobia levels of children and adolescents with epilepsy. Multi-factor ordinal logistic regression analysis was employed to identify influencing factors of physical activity levels. Results The median physical activity score for children with epilepsy was 52.00 MET (IQR: 47.00 ~ 57.00). None of the children aged 6 ~ 17 years met the minimum weekly moderate-to-vigorous physical activity (MVPA) standards recommended by the Chinese Physical Activity Guidelines for Children and Adolescents or WHO (420 minutes/week, 60 minutes/day × 7 days). The daily average sedentary time was (6.79±3.24) hours, significantly exceeding the WHO-recommended threshold (<2 hours/day).Univariate analysis demonstrated statistically significant differences in the children's physical activity levels with epilepsy based on parental perceptions of activity importance and parental encouragement for physical activity (H=15.779; H=8.034, all P<0.05). Spearman correlation analysis revealed significant positive associations between physical activity levels and activity attitudes (r=0.275), perceived behavioral control (r=0.330), and behavioral intentions (r=0.281) (all P<0.01), while kinesiophobia exhibited a significant negative correlation (r=−0.237, P<0.05). Multi-factor ordinal logistic regression analysis identified perceived behavioral control [OR=0.751, 95%CI (−0.509, −0.065)], occasional parental companionship in physical activities [OR=0.157, 95%CI (−3.660, −0.043)], and frequent parental encouragement [OR=0.000, 95%CI (−16.577, −14.272)] as protective factors for adequate physical activity (all P<0.05). Conversely, kinesiophobia emerged as a significant risk factor [OR=1.113, 95%CI (0.007, 0.207), P<0.05]. Conclusion Insufficient physical activity levels and excessive sedentary behavior are prevalent among children with epilepsy. Enhancing perceived behavioral control, increasing parental companionship during and encouragement for children's engagement in physical activities and reducing kinesiophobia may serve as critical intervention targets to improve physical activity levels in this population.