Mitochondria are essential for cellular survival and function. In neurons, mitochondria are transported to various subcellular regions as needed. Thus, defects in the axonal transport of mitochondria are related to the pathogenesis of neurodegenerative diseases, and the movement of mitochondria has been the subject of intense research. However, the inability to accurately track mitochondria with subpixel accuracy has hindered this research. Here, we report an automated method for tracking mitochondria based on the center of fluorescence. This tracking method, which is accurate to approximately one-tenth of a pixel, uses the centroid of an individual mitochondrion and provides information regarding the distance traveled between consecutive imaging frames, instantaneous speed, net distance traveled, and average speed. Importantly, this new tracking method enables researchers to observe both directed motion and undirected movement (i.e., in which the mitochondrion moves randomly within a small region, following a sub-diffusive motion). This method significantly improves our ability to analyze the movement of mitochondria and sheds light on the dynamic features of mitochondrial movement.