Background There is a greater prevalence of lower extremity malalignment in obese children during static posture; however, there has been less examination of dynamic joint function in this cohort. Therefore, the purpose of this study was to determine kinematic differences that exist between obese and non-obese children that would support previously reported static joint malalignment. Methods Forty children were classified as obese (n = 20) or non-obese (n = 20). Lower extremity joint kinematics were collected during five walking trials at a self-selected pace. Peak joint displacement and amount of joint motion throughout the gait cycle (calculated as the integrated displacement curve) were analyzed for group differences. Findings Non-obese children had greater peak knee and hip extension during gait; however, there were no group differences in the integrated sagittal displacement curve. Obese children had greater peak angular displacement and integrals of angular displacement for peak hip adduction, hip internal rotation, and foot abduction (toe-out) than non-obese children. Obese children also had greater peak knee external rotation than non-obese children. Interpretation Non-obese children showed greater range of motion in the sagittal plane, particularly at the hip and knee. Frontal and transverse plane differences suggest that obese children function in a more genu valgum position than non-obese children. Static measures of genu valgum have been previously associated with pediatric obesity; the findings indicate that there are also dynamic implications of said malalignment in obese children. Genu valgum presents increased risk of osteoarthritis for obese children and should be considered when prescribing weight bearing exercise to this cohort.