[Purpose] The present study longitudinally investigated injury occurrences and the risk factors for muscle tightness, core stability, and dynamic standing balance among junior high school student baseball players. [Subjects] Thirty-nine male students, belonging to baseball clubs at 2 junior high schools, participated in this study. [Methods] Study measurements were obtained twice, once in the early stage of the baseball season (March) and once at the end of the season (July). All subjects underwent muscle tightness testing, the Star Excursion Balance Test (SEBT), and trunk endurance testing during each measurement session. [Results] Fifteen players experienced episodes of elbow or shoulder pain while throwing. Players in the pain group demonstrated a significant increase in the tightness of their shoulder internal rotators, axis-leg quadriceps, and axis-leg hamstrings. There was no clear evidence of differences of changes in core stability and dynamic standing balance between the groups. [Conclusion] The results of this study suggest that lower extremity muscle tightness early in a season and the subsequent decline in the flexibility of the axis-leg quadriceps and hamstrings during the season may be due to an increased upper extremity load while throwing, thus producing shoulder and elbow pain.