Excessive body mass represents a serious threat to the optimal psychophysical development of children, and it is known to be able to significantly affect their locomotor capabilities, making them more prone to the development of musculoskeletal disorders. However, despite the relevant number of existing studies, a clear gait pattern of overweight children has not been defined yet, particularly in the case of a mass excess that is relatively small (i.e., in those not obese). In the present study, we employed a wearable inertial measurement unit placed on the low back to derive spatio-temporal parameters and quantify the smoothness of gait (by means of harmonic ratio) from trunk accelerations acquired during gait trials carried out by 108 children aged 6–10 (46% males), stratified into two groups according to their body mass index (normal weight, n = 69 and overweight, n = 39). The results show that while gait speed, stride length, cadence and double support duration were found to be almost identical in the two groups, significant differences were observed in terms of harmonic ratio. In particular, overweight children exhibited a reduced harmonic ratio in the antero-posterior direction and higher harmonic ratio in the medio-lateral direction. While the significantly lower harmonic ratio in the antero-posterior direction is likely to be indicative of a loss of smoothness in the walking direction, probably due to a combination of factors associated with the altered movement biomechanics, the higher harmonic ratio in the medio-lateral direction might be associated with specific strategies adopted to increase lateral stability. Although further studies are necessary to elucidate the specific mechanisms that influence the smoothness of gait, it is noteworthy that harmonic ratios appear sensitive even to subtle change in locomotor control in overweight children characterized by apparently regular spatio-temporal parameters of gait and might be employed to assess the effectiveness of interventions designed to improve mobility functions.