Schools have been postulated as ideal environments to encourage physical activity (PA). This study aimed to assess the relationship between PA in school hours, motor competence, and screen time in a sample of Spanish preschool children. Fifty-seven 4-5-year-old preschoolers (n = 32 girls) participated. The Garmin Vivofit wristband was used to measure the PA levels during school hours in a week. Sedentary behavior was estimated through screen-time hours reported by preschoolers' families and motor competence was assessed by the Athletic Skills Track. The anthropometry (weight/height) and demographic data were also collected. We found that motor competence was significantly associated with PA both in minutes and in steps. Therefore, increased motor competence was related to higher engagement in PA during school hours. No association was found between screen time and PA or proficiency of motor competence. No gender differences were found in any variable assessed. Based on the relationship between motor competence proficiency and the amount of PA in preschool children, our findings support the need for specific strategies to promote fundamental movement skills and increase PA practice from early childhood.