ABSTRACT Minimalist walking shoes have been shown to improve foot muscle size and strength in active adults, but not in our previous study involving children, which could relate to the more structured footwear used in our study. Hence, this study examined the effects of true minimalists on intrinsic foot muscle size and strength, foot arch integrity, and physical function among primary school children. After a baseline assessment, 30 primary school students aged between 9 and 12 were given a pair of minimalist shoes (minimalist index = 92%) as their regular school shoes for two school terms, followed by a re-assessment. Seventeen of the 30 participants in the minimalist group completed the study. Compared to the control group, the minimalist group showed significantly increased cross-sectional area of abductor hallucis (p = 0.047, Cohen’s d = 0.57) and flexor digitorum brevis (p = 0.037, Cohen’s d = 0.80), increased strength of the hallux (p = 0.015, Cohen’s d = 0.76) and lesser toes (p = 0.014, Cohen’s d = 0.66), greater arch height (p = 0.020, Cohen’s d = 0.52) and standing long jump distance (p = 0.001, Cohen’s d = 9.79). The control group exhibited improved standing long jump performance only (p = 0.020, Cohen’s d = 10.70). Minimalist shoes worn daily to school promote intrinsic foot muscle size and strength, and improve foot arch integrity among primary school students.