Introduction: Treadmill training is known to prevent muscle atrophy after spinal cord injury (SCI), but the training duration required to optimize recovery has not been investigated. Methods: Hemisected mice were randomized to 3, 6, or 9 weeks of training or no training. Muscle fiber type composition and fiber cross-sectional area (CSA) of medial gastrocnemius (MG), soleus (SOL), and tibialis anterior (TA) were assessed using ATPase histochemistry. Results: Muscle fiber type composition of SCI animals did not change with training. However, 9 weeks of training increased the CSA of type IIB and IIX fibers in TA and MG muscles. Conclusions: Nine weeks of training after incomplete SCI was effective in preventing atrophy of fast-twitch muscles, but there were limited effects on slow-twitch muscles and muscle fiber type composition. These data provide important evidence of the benefits of exercising paralyzed limbs after SCI.