Mitochondria, serving as the hub of energy metabolism, are essential to all biological processes. Their distribution within the body varies according to structural and functional demands. However, current strategies for regulating mitochondrial distribution remain limited. Electromagnetic waves in the terahertz (THz) frequency range have been shown to influence various biological processes, including plasma membrane dynamics and signal transmission. Given that THz radiation has been confirmed to alter the structure of phospholipid membranes, mitochondria—which share a similar membrane composition—may likewise be affected. To investigate this possibility, the effects of terahertz irradiation on mitochondrial distribution in the cortex and hippocampus of mice has been observed. To some extent, terahertz wave irradiation affected the distribution of mitochondria. These findings suggest that THz electromagnetic waves may hold potential as a novel tool for regulating mitochondrial distribution.