Changes in resting state functional connectivity are induced by sensorimotor training and assumed to be concomitant of motor learning, although a potential relationship between functional and structural connectivity associated with sensorimotor sequence learning remains elusive. To investigate whether initial structural connectivity relates to changes in functional connectivity, we evaluated resting state functional connectivity (rs-FC), white matter fibre density (FD), fibre-bundle cross-section (FC), and gray matter volume (GMV) in healthy human participants before and after two days of performing a complex whole-body serial reaction time task (CWB-SRTT). As CWB-SRTT was implicit, participants were not told about the presence of any sequence. Since the lateral prefrontal cortex (PFC) plays an important role in sequence learning, we hypothesized that structural connectivity within the PFC prior to learning is associated with changes in rs-FC involving the lateral PFC. Sequence specific improvements, as assessed by the time difference between the last random and the last sequence blocks, were observed for reaction times, suggesting that sensorimotor sequence memory was acquired. Rs-FC between the right lateral PFC and bilateral striatum increased significantly in the learning group, when compared to a control group who performed only random blocks. This indicated that rs-FC changes are related to sequence memory but not to exercise itself. In addition, changes in rs-FC between the right lateral PFC and the left striatum were correlated with sequence specific improvements in individual reaction times. Furthermore, changes in rs-FC between right lateral PFC and left striatum were positively correlated with FC in the right anterior corona radiata measured before the task. We did not find any structural changes or significant correlations in FD or GMV. These findings suggest that an early phase of sensorimotor sequence learning in complex whole-body movements is associated with an increase in rs-FC between prefrontal and subcortical regions. Furthermore, we provide novel evidence that CWB-SRTT-induced changes in rs-FC were correlated with FC within the PFC.