The purpose of this study was to evaluate the impact of the BRAINballs program on second graders’ gross motor skills in a primary school in Vietnam. A total of 55 students (23 boys and 32 girls) aged seven years participated in the study. The research used the method of a pedagogical experiment and parallel group technique (experimental and control group) with pre- and post-testing. The study was conducted in the school year 2019/2020. The gross motor skills performance was assessed by the Test of Gross Motor Development—2nd Edition. The BRAINballs program was conducted twice a week and combined physical activity with subject-related contents by means of a set of 100 balls with painted letters, numbers, and signs. The results showed that the experimental and control groups improved their motor skills after one school year (p < 0.001). However, the analysis of covariance demonstrated that students from the experimental group, compared to students from the control group, showed significantly better scores in both subtests: locomotor (p = 0.0000) and object control skills (p = 0.0000). The findings of this study show that the BRAINballs program had a positive effect on children’s motor performances and may help to better understand the development of basic motor skills of seven-year-old students in Vietnam.