Caffeine (CAF) has been shown to be an effective ergogenic aid in enhancing sports performance, including vertical jump (VJ), sprint, balance, agility, and freestyle swimming performance (FSP). However, whether acute CAF supplementation improves FSP in moderately trained female swimmers has not been well documented. Therefore, this study aimed to investigate the effects of CAF intake on vertical jump, balance, auditory reaction time (ART), and swimming performance in female swimmers. In a double-blind, cross-over design, eight moderately trained female swimmers (age: 21.3 ± 1.4 years, height: 161.2 ± 7.1 cm, body mass: 56.3 ± 6.7 kg, body mass index (BMI): 21.9 ± 1.3 kg/m2, and habitual CAF intake: 246.4 ± 111.4 mg/day) ingested caffeine (CAF) (6 mg/kg) or a placebo (PLA) 60 min before completing VJ, balance, ART, and 25/50 m FSP. CAF supplementation resulted in a significantly lower time both in 25m (p = 0.032) and 50m (p = 0.033) FSP. However, CAF resulted in no significant difference in VJ, ART, and RPE (p > 0.05). Balance test results showed a non-significant moderate main effect (d = 0.58). In conclusion, CAF seems to reduce time in short-distance swimming performances, which could be the determinant of success considering the total time of the race. Thus, we recommend coaches and practitioners incorporate CAF into swimmers’ nutrition plans before competitions, which may meet the high performance demands.