There has been enormous progress in the treatment of multiple sclerosis (MS) in recent years, but further improvement in therapy is still required because not all patients respond optimally to existing treatments. Increasing evidence has demonstrated that combination therapies produce a more favorable clinical outcome than monotherapy in MS treatment. Minocycline is effective in experimental autoimmune encephalomyelitis (EAE), and is a promising candidate for future MS medication. Glucocorticosteroids (GCS) belong to the most potent immunosuppressive drugs and are the mainstay for treatment of acute relapses in MS. In this study, we tested whether the combination of minocycline and prednisone (a synthetic GCS) at suboptimal doses could produce synergistic effects in EAE. Our findings showed that the combination of these two drugs functioned better than when they were individually administered in EAE mice, as evidenced by decreased clinical scores, reduced inflammation and demyelination, and improved magnetic resonance imaging outcomes. Further studies revealed that the combined treatment prevented the reduction of brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF) mRNA expression in cerebral cortex of EAE mice. In conclusion, our findings indicated that this combination therapy suppressed disease severity of EAE partially through blocking the downregulation of neurotrophic factor expression, suggesting that the combination of minocycline and prednisone could be a novel treatment in MS.