Lateral ankle sprain (LAS) is one of the most common sport-related injuries among basketball players. Most basketball players experience a first LAS particularly in junior high school. Thus, it is crucial to develop effective prevention strategies for LAS in junior high school populations. However, the characteristics for first-time LAS are not clear. This study aimed to compare the physical and functional characteristics of junior high school basketball players with and without a history of LAS. Two hundred and thirty-eight junior high school basketball players (128 boys and 110 girls) volunteered for this study. We asked participants to complete a self-reported injury history questionnaire. We also assessed physical functions, including range of motion, muscular strength, dynamic balance, and performance. The prevalence of LAS was 75.6% (boys: 73.4%, girls: 78.2%). Boys with a history of LAS had significantly higher height, body mass, and BMI compared to those without a history of LAS (p<0.05). Girls with a history of LAS had significantly lower scores on the star excursion balance test in the anterior reaching direction compared with the control group (p=0.015). Various measures of physical function were associated with LAS, but these associations were different between boys’ and girls’ basketball players. These findings from this study indicate that clinicians should identify sex-specific impairments associated with LAS when designing targeted intervention programs.