In the course of development children acquire various skills such as playing the piano or riding a bike. In adults, the early phases of learning are characterized by engagement of the prefrontal cortex (PFC) reflecting high control demands as strategies and new routines need to be established. We used fMRI to examine how the protracted development of the PFC contributes to age differences in motor skill learning between children (7 - 10 years) and adults. In an associative visuo-motor learning task, participants learned different sequences by repeatedly practicing them. During the early phases of learning, both children and adults showed enhanced PFC engagement. In contrast, in the late phases of learning both groupd showed greater engagement of the right motor cortex. However, the increase in activity over the course of learning was greater for adults compared to children. Representational similarity analyses revealed that the neural representations of the sequences became more similar with learning in both groups. In motor regions, representational stability increased similarly for children and adults, whereas in the PFC children showed less pronounced effects of learning than adults. These results suggest that ongoing development in control and representational systems contribute to motor sequence learning in childhood.