All Latin-American countries are affected by the lack of physical activity and its consequences on youth. Chile's population has shown troublingly low levels of moderate-to-vigorous physical activity. This is the first study using objectively measured physical activity levels in Chilean adolescents. The objectives were to compare the compliance with daily recommendations of moderate-to-vigorous physical activity between physical education and non-physical education days, and to compare physical activity levels according to gender, age and weight status. A total of 123 Chilean secondary students (52 girls and 71 boys; 13.5 ± 0.7 years old) participated in this study. Physical activity was registered by GT3X accelerometers during an entire week. Results showed that there was a significant increase in the proportion of adolescents achieving the daily recommendation of moderate-to-vigorous physical activity on physical education days (23.6%) than on non-physical education days (14.6%) (p = 0.05). Boys and older adolescents presented statistically higher levels of moderate-to-vigorous physical activity on physical education days than on non-physical education days. No differences were found in weight status comparison. Physical education has been found to be a crucial element in achieving the daily recommendations of moderate-to-vigorous physical activity. Diverse strategies in order to increase the moderate-to-vigorous physical activity in physical education according to the factors analysed are reported and discussed.