Fourteen science high school students participated in this study, which investigated neural-network plasticity associated with hypothesis-generating and hypothesis-understanding in learning. The students were divided into two groups and participated in either hypothesis-generating or hypothesis-understanding type learning programs, which were composed of 12 topics taught over a 12-week period. To measure change in student competence and brain networks, a paper & pencil test and an fMRI scanning session were administered before and after the training programs. Unlike the hypothesis-understanding group, a before and after training comparison for the hypothesis-generating group showed significantly strong changes in hypothesis explanation quotients and functional brain connectivity associated with hypothesis-generating. However, for the hypothesis-understanding group, the brain network related to hypothesis-understanding significantly strengthened, not from hypothesis-generating type learning, but from hypothesis-understanding type learning. These findings suggest that for hypothesis-generating and hypothesis-understanding there are at least two specialized brain network systems or processes at work in the brain. Furthermore, hypothesis-generating competence could be developed by appropriate training programs such as teaching by way of active hypothesis generation rather than present passive expository teaching practices.