•Minocycline was toxic to NPCs at the concentration of 20 and 40μg/ml in culture.•1, 5 and 10μg/ml minocycline suppressed NPC differentiation toward neurons.•5 and 10μg/ml minocycline impaired the pro-apoptotic effect of microglia on NPCs.•5μg/ml minocycline recovered NPC neuronal differentiation that was impaired by microglia. Neural progenitor cell (NPC) transplantation offers great potential to treat spinal cord injury (SCI), but their efficiency is limited by poor survival and neuronal differentiation after transplantation. In the injury site, microglia may become activated and participate in the inflammation reaction. In vitro studies indicated that activated microglia might impair NPC survival and neuronal differentiation, but resting microglia did not. This study investigated the potential of minocycline to modify the negative effects of activated microglia on NPCs in vitro. First, the direct effects of minocycline on NPCs were tested. The results showed that at the concentration of 10. μg/ml or lower, minocycline did not affect NPC survival and proliferation, but impaired neuronal differentiation. Then microglia were activated with lipopolysaccharide (LPS) or treated with LPS plus minocycline (LPSMC), and the effects of conditioned media on NPC apoptosis and differentiation were studied. The results showed that, compared with LPS treatment group, the microglia conditioned media of LPSMC treatment group resulted in a significantly lower apoptotic rate of NPCs, and increased the neuronal differentiation of NPCs. This suggested that minocycline might inhibit the negative effects of microglia on NPCs, and have the potential to support the survival and neuronal differentiation of transplanted NPCs for SCI.