We report that rats learning complex motor skills or exercising moderately show changes in expression of brain-derived neurotrophic factor (BDNF) and its receptor, TrkB protein, in cerebellum and motor cortex. It is now known that physical activity increases expression of some neurotrophins. We examined the time course of BDNF and TrkB expression after 1, 3, 5, 7 or 14 days in one of three conditions: (1) an “acrobatic” motor skill learning condition (AC), (2) a motor activity condition (moderately paced running on a flat track; MC) and (3) an inactive social-only control (SC) that served as a baseline group. Expression levels of BDNF and TrkB were evaluated by measuring relative optical density of the immunocytochemical reaction product. In cerebellar molecular layer, expression of BDNF correlated significantly with time spent in AC and MC over the first 7 days of training and remained elevated after 14 days of AC but not of MC. Changes in TrkB protein expression in cerebellar molecular layer mirrored those for BDNF during the first 7 days of training, but subsequently its expression subsided to the control level. In motor cortex, a significant increase in BDNF and TrkB protein expression was detected in the upper layers after 14 days in AC. Increased expression of BDNF, but not of TrkB, was observed in upper motor cortical layers after 14 days of MC. These data indicate that complex motor learning and moderate physical activity with little learning produce different effects on the expression pattern of BDNF and its receptor and may have implications for neural plasticity arising from such experiences.