Background Physical activity (PA) and screen time (ST) may influence vitamin D status in children with disabilities, yet their relationships remain understudied in this population.Methods We analyzed data from 645 children with disabilities aged 3-19 years. PA and ST were categorized into quartiles. Multiple linear regression models were used to examine associations between PA, ST, and vitamin D levels, adjusting for demographic and clinical characteristics.Results Higher PA was positively associated with vitamin D levels (beta = 0.984, 95% CI: 0.388-1.58, p = 0.003) in fully adjusted models. Participants in the highest PA quartile had significantly higher vitamin D levels compared to the lowest quartile (beta = 6.884, 95% CI: 2.736-11.031, p = 0.003). Conversely, ST showed an inverse association with vitamin D levels (beta = -0.8, 95% CI: -1.414 to -0.186, p = 0.015), with the highest ST quartile showing significantly lower vitamin D levels compared to the lowest quartile (beta = -8.098, 95% CI: -13.318 to -2.877, p = 0.005). Males were more likely to engage in high PA (66.31%), and both PA and ST showed significant age-related patterns.Conclusions Our findings reveal clear links between physical activity, screen time, and vitamin D levels in children with disabilities. Promoting physical activity and reducing screen time may be effective strategies to improve vitamin D status in this population.