This study aimed to describe the injury profiles of young Korean baseball players according to position and age as the proportion and distribution of injuries based on playing position and age remains unclear. A total of 271 elite youth baseball players aged 8 to 16 years were divided into two groups: elementary school (ES) (n = 135) and middle school (MS) (n = 136). The participants' basic, baseball practice, and injury information were collected. Injuries in the MS group were not limited to the elbow and shoulder, and injury prevalence varied by age group and baseball position. The most injured body region in the ES group was the elbow joint, regardless of the position. In contrast, the most injured body region in the MS group was the lower back, except for infielders whose elbows were the most injured. Additionally, the MS group was more likely to experience injuries to the lower back (OR = 4.27, 95% CI = 2.47-7.40), shoulder (OR = 1.93, 95% CI = 1.08-3.43; p = 0.024), and knee (OR = 2.15, 95% CI = 1.17-3.94; p = 0.012). Our findings indicate that excessive practice and a lack of rest during MS (growth spurt period) can significantly increase the risk of lower back problems in young baseball players.