Knowledge about associations between school-based initiatives and physical activity patterns is limited. The purpose of this paper was to examine associations between factors in the school environment, physical activity and sedentary time during school time. The cross-sectional study included 1139 adolescents aged 13–14 from 34 schools. Physical activity and sedentary time were measured using hip-worn accelerometers. Factors in the school environment included health policy, a mobile phone ban during breaks, organized physical activities during breaks and activity breaks during lessons reported by teachers. The frequency and duration of breaks and physical education (PE) lessons were collected from school schedules. The results showed significant associations between health policy (β = 3.87, 95% confidence interval (CI): 2.37, 5.23), the mobile phone ban (β = 2.51, 95% CI: 1.29, 3.94) and PE; total duration (β = 0.08, 95% CI: 0.05, 0.11), average duration (β = 0.08, 95% CI: 0.01, 0.13) and frequency (β = 1.73, 95% CI: 0.50, 3.04) and moderate-vigorous physical activity. There were negative associations between health policy (β = −6.41, 95% CI: −10.24, −2.67), the mobile phone ban (β = −3.75, 95% CI: −7.25, −0.77) and PE; total duration (β = −0.15, 95% CI: −0.23, −0.08) and average duration (β = −0.14, 95% CI: −0.27, −0.03) and time spent sedentary. Adolescents attending schools with health policies, mobile phone bans and more time for PE showed higher levels of physical activity and lower sedentary time.