Objectives. To determine the proportion of primary school students who fulfill the World Health Organization (WHO) recommendations on physical activity and the factors associated with less time of moderate-intense physical activity in urban areas of three cities in Peru. Materials and methods. Cross-sectional study with a random selection of schoolchildren aged 6 to 13 from public educational institutions in urban areas of Chiclayo, Huaraz and Tarapoto. In order to measure the time and intensity of physical activity, schoolchildren were given an accelerometer for a week. Furthermore, nutritional conditions were evaluated through the calculation of their body mass index. Results. A total of 1241 schoolchildren of both sexes aged between 6 and 13 years participated. 40% of schoolchildren in Chiclayo, 56% in Tarapoto and 66% in Huaraz fulfilled the WHO recommendations to perform at least 60 minutes of moderate-intense physical activity per day. The intensity of physical activity was significantly higher in younger schoolchildren and males. It was also found that the factors associated with fewer minutes of moderate-intense physical activity per day were schoolchildren of older age, females, with an obesity condition, whose mothers had higher educational level, and lived in Chiclayo or Tarapoto (p <0.05). Conclusions. Nearly 50% of schoolchildren meet the WHO recommendation on daily physical activity, the less active groups were older schoolchildren, obese and female; therefore, actions should be focused on them to promote adequate physical activity habits.