Modified invasion games promote the development of real and perceived motor competence. Children with higher motor competence are more likely to participate in physical activity practice and to remain in it, both in adolescence and adulthood. (1) Background: The purpose of this study is to determine the effect of modified invasion games on the real motor competence and self-assessment of the physical condition fifth-grade students from a private school in Viña del Mar, Chile. (2) Methods: 40 girls and boys with an average age of 11.47 years (SD = 0.554) participated in this study during a 12-week intervention. The MOBAK 5-6 battery was used to assess actual motor competence, the SEMOK questionnaire was used to determine perceived motor competence, the International Fitness Scale (IFIS) self-assessment questionnaire was used to assess perceived physical fitness, and the weight/size ratio was used to determine BMI. A Friedman’s nonparametric ANOVA analysis was applied to determine the effect of the intervention, in addition to an analysis of covariance (ANCOVA) to identify the influence of the covariates on motor competence. (3) Results: No statistically significant differences were established between weight, BMI, and waist circumference. There was a statistically significant difference after the intervention in the actual motor competence of object control (p = 0.005) and perceived motor competence of object control (p ≤ 0.001) (4) Conclusions: An intervention based on modified invasion games is effective for the improvement of actual and perceived motor competence of object control. It was not possible to identify a positive effect on the self-assessment of muscle strength after the intervention.