Intrinsic functional connectivity from resting state functional magnetic resonance imaging (rsfMRI) has increasingly received attention as a possible predictor of cognitive function and performance. In this study, we investigated the influence of practicing skillful tool manipulation on intrinsic functional connectivity in the resting brain. Acquisition of tool-use skill has two aspects such as formation of motor representation for skillful manipulation and acquisition of the tool concept. To dissociate these two processes, we chose chopsticks-handling with the non-dominant hand. Because participants were already adept at chopsticks-handling with their dominant hand, practice with the non-dominant hand involved only acquiring the skill for tool manipulation with existing knowledge. Eight young participants practiced chopsticks-handling with their non-dominant hand for 8 weeks. They underwent functional magnetic resonance imaging (fMRI) sessions before and after the practice. As a result, functional connectivity among tool-use-related regions of the brain decreased after practice. We found decreased functional connectivity centered on parietal areas, mainly the supramarginal gyrus (SMG) and superior parietal lobule (SPL) and additionally between the primary sensorimotor area and cerebellum. These results suggest that the parietal lobe and cerebellum purely mediate motor learning for skillful tool-use. This decreased functional connectivity may represent increased efficiency of functional network.