Brain Breaks Physical Activity Solutions (BBPAS) is a web-based structured physical activity (PA) video that is specifically designed for school settings and can stimulate a student’s health and learning. The purpose of this study is to measure the effect of BBPAS on the stages of change, decisional balance, processes of change, self-efficacy and leisure-time exercise among Malay ethnic primary school children. A validated Malay version of three of the five constructs was derived with sound validity and was used in the present study. A total of 159 male and 163 female children aged 10 to 11 years old, mean (SD) = 10.53 (0.50), were recruited from two schools in Kelantan, Malaysia. Purposive sampling was used to divide the children into intervention (n = 177) and control (n = 145) groups. Children in the intervention group underwent BBPAS activity for an accumulated 30 min per week, while children in the control group were not involved in the BBPAS intervention. Mixed factorial analysis of variance (ANOVA) was used to examine the effect of BBPAS on the study variables. A mixed ANOVA showed significant changes (time effect) on cognitive process, F(1, 320) = 5.768, p-value = 0.017; behavioural process, F(1, 313) = 5.736, p-value = 0.017; and internal feeling, F(1, 312) = 6.050, p-value = 0.014. There was also a significant difference between groups on cons, F(1, 316) = 7.504, p-value = 0.007. A significant interaction effect was observed for stages of change, F(1, 319) = 7.861, p-value = 0.005; pros, F(1, 316) = 31.311, p-value = 0.001; internal feeling, F(1, 312) = 4.692, p-value = 0.031; and behavioural process, F(1, 313) = 7.312, p-value = 0.007. In conclusion, BBPAS was successful in improving four of the five constructs, and thus, should be recommended to be used in schools throughout Malaysia.