Low motor competence (MC) can cause low participation in physical activities in preschool children, and together with a high caloric intake, it can lead to obesity. Interventions on motor skills are effective in the short term to improve MC, therefore the objectives of this study were (1) to investigate the effect of a short six-week program on levels of motor competence in preschool children, and (2) to examine the effects of gender-based intervention. A total of 156 preschool children (5.20 ± 0.54 years old) from Lugo (Spain) participated. A quasi-experimental pre–post-test design was used with a control group of 76 students. The Movement Assessment Battery for Children—2nd Edition (MABC-2) was used to collect the data. Significant differences between the control and experimental groups were found after the intervention program in aiming and catching (p < 0.001), balance (p < 0.001), the total score of eight tests (p < 0.001), and total percentile score (p < 0.001). The results regarding gender in the experimental group showed a reduction in differences with respect to the initial results except in aiming and catching, where scores were higher in boys. The data suggest that the application of specific intervention programs in MC could positively influence the improvement of MC in preschool children, thus reducing differences between genders.