Individual learning performance of cognitive function is related to functional connections within 'task-activated' regions where activities increase during the corresponding cognitive tasks. On the other hand, since any brain region is connected with other regions and brain-wide networks, learning is characterized by modulations in connectivity between networks with different functions. Therefore, we hypothesized that learning performance is determined by functional connections among intrinsic networks that include both task-activated and less-activated networks. Subjects underwent resting-state functional MRI and a short period of training (80-90 min) in a working memory task on separate days. We calculated functional connectivity patterns of whole-brain intrinsic networks and examined whether a sparse linear regression model predicts a performance plateau from the individual patterns. The model resulted in highly accurate predictions (R(2) = 0.73, p = 0.003). Positive connections within task-activated networks, including the left fronto-parietal network, accounted for nearly half (48%) of the contribution ratio to the prediction. Moreover, consistent with our hypothesis, connections of the task-activated networks with less-activated networks showed a comparable contribution (44%). Our findings suggest that learning performance is potentially constrained by system-level interactions within task-activated networks as well as those between task-activated and less-activated networks.