As athletes pursue excellence, training techniques continue to advance, making structured physical activity an essential tool for enhancing performance. To optimize athletic performance in modern competitive sports, the balance of physical performance and mental clarity is required. This study seeks to examine the effects of High-Intensity Interval Training (HIIT) on cognitive and physical skills in basketball and soccer players. A 3-week HIIT protocol was incorporated based on the Wingate technique. This study included 10 soccer players and 10 basketball players with an average age of 22.79 ± 1.90 years. Participants performed pre- and post-intervention assessments. Physical proficiency was assessed using 20 m sprint, change-of-direction (COD) and dribbling tests, while cognitive skills were assessed using motion object tracking (MOT), working memory, perceptual load (PL), and attention window (AW) tests. The HIIT intervention significantly improved cognitive performance in particular; noteworthy observations were a 15% improvement in motion object tracking test scores and a 16% increase in working memory test scores for basketball players. The attention window test scores showed a 32% increase, and perceptual load test scores were 31% decreased for soccer players post-intervention. There were significant improvements in physical skills; for example, sprint times were decreased by 6%, and change-of-direction and dribbling times were reduced by 8% and 7%, respectively, indicating improved agility, speed, and ball control abilities. In conclusion, both groups performed significantly better on cognitive and physical skill tests post-HIIT intervention.