This study assessed the physical development, physical fitness (muscular endurance, muscular strength, flexibility, agility, power, balance), and basal metabolic rate (BMR) in a total of 4410 children aged six (73–84 months) residing in Korea. Their physical fitness was visually classified according to the physical fitness factor and—considering that children showed great variations in the physical fitness criteria depending on their physique and body composition—the study aimed to assess characteristics such as physique and BMR, the precursor for fat-free mass, based on the physical health clusters selected through a multivariate approach. As a result, the physical health clusters could be subdivided into four clusters: balance (1), muscular strength (2), low agility (3), and low physical fitness (3) cluster. Cluster 1 showed a high ratio of slim and slightly slim children, while cluster 2 had a high proportion of children that were obese, tall, or heavy, and had the highest BMR. We consider such results as important primary data for constituting physical fitness management programs customized to each cluster. It seems that it is necessary to have a multidirectional approach toward physical fitness evaluation and analysis methodologies that involve various physical fitness factors of children.