Maxillary first premolars have a unique shape because of their curvature features, positional relationship of the cusps, and most prominent points, making them different from other teeth. This study aimed to quantitatively analyze the detailed three-dimensional morphometric structure of maxillary first premolars and sexual dimorphism. The study participants were 60 elementary and junior high school students (30 boys and 30 girls) in Japan. The distance between landmarks was measured using the three-dimensional coordinates of plaster casts, and the data collected was statistically analyzed. Sexual dimorphism was greater in the lingual cusp, showing greater variation in size than the buccal cusp. Boys exhibited significantly larger relative distances in the mesiodistal and buccolingual directions than girls; particularly, regarding mesiodistal diameter of the central groove, mesial slope of the buccal cusp, and distal slope of the lingual cusp. These results may be due to a slight difference in the timing of secondary enamel knots between boys and girls during the developmental stage, which was reflected in the sexual dimorphism of the completed teeth. Curvature features, cusp positions, and most prominent points were considered individual traits because they were not interrelated. Subtle differences during the developmental stage may lead to sexual dimorphism of the completed crown. Furthermore, the morphological characteristics of the maxillary first premolars may be related to their location in the dental arch.