The sphenoid sinus (SS) is located close to vital structures, such as the pituitary gland, and it has significant clinical relevance. This study aimed to clarify the growth pattern of the SS in Japanese children using three-dimensional computed tomography (CT). Seventy-eight participants with congenital, acquired, or external auditory canal cholesteatoma were recruited and underwent CT more than twice during their treatment. Using the volume-rendered images, the size and volume of the SS were measured. Furthermore, on the scout image, the morphological measurements of the cranial base were determined. The size and volume of the SS increased with age, and peaked at the mean age of 15 years. For males, the volume of the SS was smaller than that of females aged <5 years. The growth rate of the SS was significantly higher in males than in females. The maximum growth rate was detected at the age of 12 years for males and 10 years for females. For females, the increase in the length of the anterior cranial base ceased at approximately 10 years of age and remained constant thereafter. In contrast, for males, the length of the anterior cranial base increased gradually until 15 years of age. Considering the similarity of the periods between the adolescent growth spurt and the maximum growth rate of the SS, changes in the size of the SS may be used as an indicator of the physical growth spurt.