Background In blast wave injury and high-energy traumatic brain injury, shock waves (SW) play an important role along with cavitation phenomena. However, due to lack of reliable and reproducible technical approaches, extensive study of this type of injury has not yet been reported. The present study aims to develop reliable SW-induced brain injury model by focusing micro-explosion generated SW in the rat brain. Methods Adult male rats were exposed to single SW focusing created by detonation of microgram order of silver azide crystals with laser irradiation at a focal point of a truncated ellipsoidal cavity of 20 mm minor diameter and the major to minor diameter ratio of 1.41 after craniotomy. The pressure profile was recorded using polyvinylidene fluoride needle hydrophone. Animals were divided into three groups according to the given overpressure: Group I: Control, Group II: 12.5±2.5 MPa (high pressure), and Group III: 1.0±0.2 MPa (low pressure). Histological changes were evaluated over time by hematoxylin-eosin staining. Findings Group II SW injuries resulted in contusional hemorrhage in reproducible manner. Group III exposure resulted in spindle-shaped changes of neurons and elongation of nucleus without marked neuronal injury. Conclusions The use of SW loading by micro-explosion is useful to provide a reliable and reproducible SW-induced brain injury model in rats.