Here we provide a standardized protocol for performing distal middle cerebral artery occlusion (DMCAO) in mice. DMCAO is a method of inducing permanent focal ischemia that is commonly used as a rodent stroke model. To perform DMCAO a temporal craniotomy is performed, and the middle cerebral artery (MCA) is permanently ligated at a point downstream of the lenticulostriate branches. The size of the lesion produced by this surgery is strain dependent. In C57BL/6J mice, DMCAO produces an infarct predominantly restricted to the barrel region of the somatosensory cortex, but in BALB/cJ mice, DMCAO generates a much larger lesion that incorporates more of the somatosensory cortex and part of the M1 region of the motor cortex. The larger lesion produced by DMCAO in BALB/cJ mice produces a clearer sensorimotor deficit, which is useful for investigating recovery from stroke. We also describe how to modify DMCAO in C57BL/6J mice with the application of hypoxia to generate a lesion and sensorimotor deficit that are similar in size to those produced by DMCAO alone in BALB/cJ mice. This is extremely useful for stroke experiments that require a robust sensorimotor deficit in transgenic mice created on a C57BL/6J background.