Phase angle, calculated as the arc-tangent of the reactance-to-resistance ratio in bioelectrical impedance analysis, represents skeletal muscle quality, and is suggested to be an indicator of sports ability and physical fitness. However, it is unclear whether phase angle is related to physical fitness in early childhood in Japanese subjects. The purpose of this study was to examine the cross-sectional relationship between physical fitness and bioelectrical impedance analysis-based phase angle in 6-year-old Japanese children. The subjects were 85 kindergarten students who participated in a physical fitness test and body composition assessment in 2017, 2018 or 2019, in the third year of kindergarten. Fitness tests included grip strength, standing long jump, and 25 m run. A multi-frequency composition analyzer was used for body composition analysis, and the phase angle of the left half of the body was acquired at 50 kHz. Statistical analysis was performed using a general linear model to calculate the regression coefficient of phase angle for physical fitness. Phase angle correlated significantly with the standing long jump and 25 m run. The regression coefficient (±standard error) of phase angle in the standing long jump in the fully adjusted model was 5.098 ±2.264 (p<0.05), and that in the 25 m run was -0.179 ±0.088 (p<0.05). There was no significant correlation between phase angle and grip strength. These results suggest that phase angle based on bioelectrical impedance analysis might be related to lower limb muscle function and running ability in 6-year-old Japanese children.