Introduction: The transtheoretical model (TTM) is an integrative model of intentional change consisting of stages of change, processes of change, decisional balance and self-efficacy. This study aimed at validating the TTM questionnaires on physical activity for Malaysian children using confirmatory factor analysis. Methods: The participants were 381 Malay students (188 male; 193 female), aged 10–12 years old, with a mean age of 10.94 (SD = 0.81). The original version of the TTM was translated into the Malay language using forward and backward translation. Certain phrases were adapted based on the local culture and vocabulary suitable for primary school students. Results: The final measurement models and their fit indices were: processes of change (CFI = 0.939, TLI = 0.925, SRMR = 0.040, RMSEA = 0.030); decisional balance (CFI = 0.897, TLI = 0.864, SRMR = 0.045, RMSEA = 0.038); and self-efficacy (CFI = 0.934, TLI = 0.915, SRMR = 0.042, RMSEA = 0.032). Conclusion: Care must be taken when using the TTM with children, as it has been prevalently validated with adults. The final version of the TTM questionnaire for Malay primary school children had 24 items for process of changes, 13 items for self-efficacy and 10 items for decisional balance.