Lateral ankle sprain (LAS) is a common sports injury that frequently occurs in active individuals. LAS is characterized by a high recurrence rate, with a large proportion of patients progressing to chronic ankle instability (CAI). Pilates exercises have provided positive results in health care and in rehabilitation. This study compared Pilates training (PT) with traditional balance training (BT) in patients with CAI. Fifty-one college football players with CAI, divided into PT ( = 26) and BT ( = 25) groups, were included in the study. The groups performed PT or BT training as assigned, three times per week for 6 weeks. Isokinetic ankle strength, one-leg hop tests, Y-balance test (YBT), and foot and ankle outcome score (FAOS) were evaluated before and after training. There were considerable improvements in both the PT and BT groups after training. Group and time comparisons revealed that the PT group achieved better triple hop test results than the BT group, whereas the BT group exhibited a greater improvement in YBT posteromedial and posterolateral reach distances. In athletes with CAI, both PT and BT effectively improved symptoms and function. These findings suggest that ankle strength, balance, and core stability should be comprehensively evaluated and targeted in CAI rehabilitation programs.