Background: Although warm-ups before exercise are widely accepted, research on sex differences in improving hamstring flexibility is limited. Differences in the physical and physiological characteristics between males and females may result in different responses to warm-ups. Objects: This study aimed to examine sex differences in the effects of specific warm-up on hamstring flexibility. Methods: This study included 24 young adults with hamstring tightness. The participants performed five maximal knee extensions and flexions at 90° flexion of the hip, and the maximal knee extension angle was measured in real-time using a smartphone clinometer application. Results: The groups did not significantly affect the maximal knee extension angle but showed a significant effect for repetition (p = 0.002) and group-repetition interaction (p = 0.002). Males had no significant change in hamstring flexibility; however, females showed a significant increase in flexibility in the 5th trial compared with the 1st trial (p = 0.041). These results demonstrated sex-specific differences in flexibility improvement over time. Conclusion: The findings of this study suggest that specific warm-up can successfully improve hamstring flexibility in females. This may be due to various factors, such as muscle stiffness of the lower extremity, estrogen levels, and temperature sensitivity. In clinical settings, specific warm-up might be helpful for females who participate in sports or activities, such as running or jumping, which require a full range of motion in the hip and knee joints.