Many studies have confirmed that activation of microglia is detrimental to the survival of new neurons and that inhibition of the inflammatory response generated by microglia activation has a protective effect on neuroregeneration after, for example, epilepsy and radiation therapy. This study is the first to explore the protective effect of long-term minocycline application on endogenous neuroregeneration after cerebral ischemia and its improvement of post-ischemic neurological function through histological and behavioral approaches. In this study, a rat model of focal cerebral ischemia was used, and minocycline was continuously administered intraperitoneally for 4 weeks at 4 days post-ischemia (outside the effective protection time window). Endogenous neural stem cells were labeled with BrdU continuously for 4-7 days after ischemia, and the differentiation of neural stem cells, the survival of new neurons and the number of activated microglia in the hippocampal region were examined histologically after 4 weeks, and the volume of cerebral infarction was calculated by stereology and measured by Forelimb Use Asymmetry Test. Horizontal Ladder Test, Rotor Rod and Water Maze were used to compare the modification of neurological function after minocycline treatment by behavioral means. Although continuous intraperitoneal injection of minocycline for 4 weeks after 4 days of ischemia did not show a reduction in infarct volume, the number of activated microglia in the hippocampal dentate gyrus was significantly reduced. Meanwhile, continuous 4-week minocycline treatment did not increase the proliferative activity of neural stem cells in the hippocampal dentate gyrus, but the number of post-ischemic surviving neurons (BrdU+/NeuN+) was significantly increased. Finally, the present study confirmed significant improvements in cognitive dysfunction such as motor function, learning and memory in ischemic rats after minocycline treatment by a series of behavioral assays. Long-term application of minocycline beyond the effective protective time window of cerebral ischemia still had an effect on improving neurological function, and this effect was associated with a decrease in the number of activated microglia and an increase in the number of regenerating neurons in the hippocampal dentate gyrus after minocycline treatment. Thus, long-term application of minocycline may have the effect of improving the microenvironment on which regenerating neurons depend, but the detailed mechanism needs to be further investigated.