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Background and objective: Tightness of the gastroc–soleus muscle complex is one of the limiting factors of the ankle joint’s range of motion (ROM) during daily activities. The aim of this study was to investigate the effectiveness of functional and extra-functional stretching of the gastrocnemius–soleus complex on knee joint loading in athletes with limited ankle dorsiflexion. Material and methods: In this cross-sectional study, 30 male athletes with gastrocnemius–soleus shortness were recruited and randomly divided into three equal-size groups of functional stretching, extra-functional stretching, and a control group. The extra-functional stretching group performed stretching exercises three times per day for eight weeks. The functional stretching group was instructed to change their gait pattern via increased heel strike during daily activities. Results: None of the stretching programs reduced the knee flexion angle in heel contact (p > 0.05). The knee flexion angle was significantly increased in the stance phase in the functional group (p ≤ 0.05). Walking speed was increased significantly in the extra-functional group (p ≤ 0.05). The knee adductor moment and external rotation moment decreased significantly in the functional group (p ≤ 0.05). Conclusion: An eight-week functional stretching program in this study led to a reduction of knee loading in the frontal and horizontal planes in comparison to the extra-functional stretching group, demonstrating the effectiveness of functional stretching in improving knee joint biomechanics during walking.