Abstract Background The effect of footwear on the gait of children is poorly understood. This systematic review synthesises the evidence of the biomechanical effects of shoes on children during walking and running. Methods Study inclusion criteria were: barefoot and shod conditions; healthy children aged ≤ 16 years; sample size of n > 1. Novelty footwear was excluded. Studies were located by online database-searching, hand-searching and contact with experts. Two authors selected studies and assessed study methodology using the Quality Index. Meta-analysis of continuous variables for homogeneous studies was undertaken using the inverse variance approach. Significance level was set at P < 0.05. Heterogeneity was measured by I2. Where I2 > 25%, a random-effects model analysis was used and where I2 < 25%, a fixed-effects model was used. Results Eleven studies were included. Sample size ranged from 4-898. Median Quality Index was 20/32 (range 11-27). Five studies randomised shoe order, six studies standardised footwear. Shod walking increased: velocity, step length, step time, base of support, double-support time, stance time, time to toe-off, sagittal tibia-rearfoot range of motion (ROM), sagittal tibia-foot ROM, ankle max-plantarflexion, Ankle ROM, foot lift to max-plantarflexion, 'subtalar' rotation ROM, knee sagittal ROM and tibialis anterior activity. Shod walking decreased: cadence, single-support time, ankle max-dorsiflexion, ankle at foot-lift, hallux ROM, arch length change, foot torsion, forefoot supination, forefoot width and midfoot ROM in all planes. Shod running decreased: long axis maximum tibial-acceleration, shock-wave transmission as a ratio of maximum tibial-acceleration, ankle plantarflexion at foot strike, knee angular velocity and tibial swing velocity. No variables increased during shod running. Conclusions Shoes affect the gait of children. With shoes, children walk faster by taking longer steps with greater ankle and knee motion and increased tibialis anterior activity. Shoes reduce foot motion and increase the support phases of the gait cycle. During running, shoes reduce swing phase leg speed, attenuate some shock and encourage a rearfoot strike pattern. The long-term effect of these changes on growth and development are currently unknown. The impact of footwear on gait should be considered when assessing the paediatric patient and evaluating the effect of shoe or in-shoe interventions.