A wealth of evidence has shown that acute aerobic exercise can enhance executive function. However, empirical evidence lacks consensus regarding whether acute aerobic exercise has a beneficial effect on cognitive flexibility when individual baseline cognitive differences are considered. Therefore, the aim of our study was to examine the effects of high-intensity interval exercise (HIIE) and moderate-intensity continuous exercise (MICE) on cognitive flexibility in young adults with differences in baseline cognitive performance. One hundred and ten college students (mean age = 20.17 ± 1.15 years) were divided into lower-performers (n = 55) and higher-performers (n = 55) groups based on their cognitive performance on the pre-test of the first cognitive flexibility test. Both groups were asked to complete a more-odd shifting task, which assesses cognitive flexibility, before and approximately 5 min after a 20 min HIIE session, a 20 min MICE session, and a reading control session. The results showed that individuals with lower baseline cognitive performance gained greater cognitive flexibility benefits from the 20 min HIIE and the 20 min MICE, whereas those with higher baseline cognitive performance had improved cognitive flexibility only from the 20 min HIIE. These findings indicate that baseline cognitive performance is a variable that influences the beneficial effects of acute exercise on cognitive flexibility. We recommend that young adults should consider their individual cognitive capacity when adopting effective and appropriate exercise modalities to improve cognitive performance.