[Purpose] Medial longitudinal arch (MLA) height is associated with various injuries and diseases and gender differences, if any. This study aimed to examine factors affecting the MLA height associated with gender differences in healthy subjects with no orthopedic disorders. [Subjects and Methods] This study included 36 healthy adults (19 males, 17 females; mean age, 21.8 ± 3.6 years; body mass index, 21.1 ± 2.0 kg/m2). Their height, body weight, foot length, muscle strength of the tibialis posterior muscle (TPM), toe-gripping strength, hallux valgus angle, inversion microdactylia angle, angle of leg–heel alignment, femoro-tibial angle, and navicular height were measured. Correlation between the ratio of arch height and other measurement parameters was examined. [Results] In females, the ratio of arch height was significantly positively correlated with muscle strength of the TPM and toe-gripping strength and negatively correlated with the hallux valgus angle and the leg-heel alignment, whereas in males, only a positive correlation between the ratio of arch height and muscle strength of the TPM was observed. [Conclusion] These results reveal that etiological mechanisms determining MLA height are different between males and females. Overall, the present results indicate that further studies identifying causes of MLA height variation must include gender-based analysis.