Prognathism in the human facial skeleton is generally divided into two types: alveolar and facial. The degree of alveolar prognathism has conventionally been evaluated using the alveolar profile angle, defined on the basis of the line through the nasospinale and prosthion and the Frankfort horizontal (FH). Previous examinations of Japanese crania from the protohistoric Kofun period (c. 300–700 AD) to the modern period have established that the medieval (c. 1200–1600 AD) Japanese possessed the strongest alveolar prognathism. However, the nasospinale is an ambiguous landmark that is difficult to determine. Moreover, it has been suggested that the alveolar profile angle itself is problematic for quantifying alveolar prognathism. Here, we devised a new method for evaluating each type of prognathism independently and investigated temporal changes in the Japanese population using three-dimensional (3D) coordinate landmark data collected with a 3D contact digitizer. Facial prognathism was quantified using an obtuse angle, termed the midfacial protrusion angle, created by a line that runs through the nasion and subspinale with the FH. Alveolar prognathism was evaluated using a reflex angle, named the alveolar protrusion angle, formed between the nasion–subspinale and subspinale–prosthion lines. An analysis of 66 male crania derived from the northern Kyushu and Yamaguchi (westernmost part of Honshu) region showed no significant change of the alveolar protrusion angle over time from the Kofun period to the modern period. In contrast, the midfacial protrusion angle increased from the Kofun period to the medieval period and then decreased in the modern period. These results suggest that the strongest facial prognathism was exhibited in the medieval period. Previous results, which suggested that alveolar prognathism was strong in the medieval Japanese, may have been significantly affected by facial prognathism.