Amphetamine (AM) treatment has been shown to alter behavioral recovery after ischemia caused by embolism, permanent unilateral occlusion of the common carotid and middle cerebral arteries, or unilateral sensorimotor cortex ablation in rats. However, the behavioral results are inconsistent possibly due to difficulty controlling the size of the lesion before treatment. There is also evidence that AM promotes neuroregeneration in the cortex contralateral to the infarction; however, the effects of AM in the ipsilateral cortex remain unclear. The purpose of this study was to employ T2-weighted imaging (T2WI) to establish controlled criteria for AM treatment and to examine neuroregenerative effects in both cortices after stroke. Adult rats were anesthetized, and the right middle cerebral artery was ligated for 90 min to generate lesions in the ipsilateral cortex. Animals were separated into two equal treatment groups (AM or saline) according to the size of infarction, measured by T2WI at 2 days after stroke. AM or saline was administered to stroke rats every third day starting on day 3 for 4 weeks. AM treatment significantly reduced neurological deficits, as measured by body asymmetry and Bederson's score. T2WI and diffusion tensor imaging (DTI) were used to examine the size of infarction and axonal reinnervation, respectively, before and following treatment on days 2, 10 and 25 after stroke. AM treatment reduced the volume of tissue loss on days 10 and 25. A significant increase in fractional anisotropy ratio was found in the ipsilateral cortex after repeated AM administration, suggesting a possible increase in axonal outgrowth in the lesioned side cortex. Western analysis indicated that AM significantly increased the expression of synaptophysin ipsilaterally and neurofilament bilaterally. AM also enhanced matrix metalloproteinase (MMP) enzymatic activity, determined by MMP zymography in the lesioned side cortex. qRT-PCR was used to examine the expression of trophic factors after the 1st and 2nd doses of AM or saline injection. The expression of BDNF, but not BMP7 or CART, was significantly enhanced by AM in the lesioned side cortex. In conclusion, post-stroke treatment with AM facilitates behavioral recovery, which is associated with an increase in fractional anisotropy activity, enhanced fiber growth in tractography, synaptogenesis, upregulation of BDNF, and MMP activity mainly in the lesioned cortex. Our data suggest that the ipsilateral cortex may be the major target of action in stroke brain after AM treatment.