Aging and physical inactivity lead to histochemical changes in muscles. The expression of many muscle proteins, including brain-derived neurotrophic factor (BDNF), silent information regulator of transcription 1 (SIRT1), and peroxisome proliferator-activated receptor γγ coactivator-1α (PGC-1a), declines with age. However, the effect of aerobic exercise on muscle structure and the expression profile of these proteins in elderly rats is unknown. Here, we investigated whether short-term aerobic exercise improves muscle structure and increases BDNF, SIRT1, and PGC-1a levels in aged rats. Ten male Wistar rats (95-week-old) were assigned to sedentary (SED) or exercise (Ex) groups. The Ex group performed running on a treadmill for 1 h, 6 times per week, for 2 weeks. The extensor digitorum longus muscles were removed to examine the muscle fibre type composition, cross-sectional area, and capillary-to-fibre (C/F) ratio. BDNF, SIRT1, and PGC-1a levels were evaluated by western blotting. Relative to the SED group, the Ex group showed increased proportion of Type I fibres (P<0.05), cross-sectional area of all muscle fibre types (P<0.05), succinate dehydrogenase activity (P<0.001), C/F ratio (P<0.05), and expression of BDNF, SIRT1, and PGC-1a (P<0.05).Thus, 2 weeks of aerobic exercise is sufficient to improve muscle histology and hypertrophic marker protein expression, indicating that it could prevent skeletal muscle atrophy in elderly rats.