Background: After-school physical activity (PA) programs promote PA among youth. Few studies have used socio-ecological health models to identify barriers and facilitators of after-school PA programs. This study examined which socio-ecological factors are associated with having an after-school PA program. Methods: A questionnaire was administered to key representatives of 114 elementary and 129 secondary schools. The association between socio-ecological factors and having an after-school PA program was analyzed at school level. Results: In both types of schools more knowledge about community schools was positively associated with having an after-school PA program (odds ratio [OR] = 1.96; 95% confidence interval [CI] = 1.18-3.27; OR = 1.88; 95% CI = 1.27-2.80, respectively). In elementary schools, environmental factors associated with having an after-school PA program included PA facilities (OR = 4.98; 95% CI = 1.08-23.05), a PA working group (OR = 3.37; 95% CI = 1.02-11.10), agreements with the community (OR = 1.60; 95% CI = 1.05-2.43), shortage of human resources (OR = 0.57; 95% CI = 0.37-0.89) and lack of support from teachers (OR = 0.51; 95% CI = 0.33-0.80). In secondary schools, environmental factors included the presence of a remunerated coordinator (OR = 5.12; 95% CI = 1.38-19.10) and partnerships with "sport and PA leaders" (OR = 3.54; 95% CI = 1.01-12.41). Conclusion: Having an after-school PA program was associated with personal and environmental factors, which supports the use of socio-ecological frameworks for explorative and intervention studies aiming to increase after-school PA programs. (Contains 3 tables.)