Body-machine interfaces, i.e. interfaces that rely on body movements to control external assistive devices, have been proposed as a safe and robust means of achieving movement and mobility; however, how children learn these novel interfaces is poorly understood. Here we characterized the learning of a body-machine interface in young unimpaired adults, two groups of typically developing children (9-year and 12-year olds), and one child with congenital limb deficiency. Participants had to control the end-effector of a robot arm in 2D using movements of the shoulder and torso. Results showed a striking effect of age - children had much greater difficulty in learning the task compared to adults, with a majority of the 9-year old group unable to even complete the task. The 12-year olds also showed poorer task performance compared to adults (as measured by longer movement times and greater path lengths), which were associated with less effective search strategies. The child with congenital limb deficiency showed superior task performance compared to age-matched children, but had qualitatively distinct coordination strategies from the adults. Taken together, these results imply that children have difficulty learning non-intuitive interfaces and that the design of body-machine interfaces should account for these differences in pediatric populations.