The aim of the present study was to evaluate the effects of caffeine ingestion and partial sleep deprivation at the end of night on cognitive and physical performance. In randomised order, fourteen football players (age: 23.57 ± 1.98 years; body weight: 59.57 ± 4.29 kg; height: 174.35 ± 5.07 cm) completed four test sessions at 08:00 h: after placebo or 3 mg·kg−1 of caffeine ingestion during a reference night, RN (bed time: from 22:30 h to 07:00 h) or a night of partial sleep deprivation, PSD (bed time: from 22:30 h to 03:00 h). During each test session, participants assessed vigilance and reaction times and performed a series of tests: cancelation test, squat jumps (SJ), and the 30-s Wingate test (for the measurement of peak power, PP, and mean power, PM). During RN, results showed that PP, PM, SJ, and vigilance increased after caffeine ingestion in comparison with placebo (p < 0.001). Moreover, both simple and choice reactions were significantly better after caffeine ingestion in comparison with placebo ingestion (p < 0.05 and p < 0.001, respectively). Results showed that reaction time, vigilance, and SJ were affected by PSD, even though PP, PM, and SJ were not affected, the following day at 08:00 h. During the PSD condition, PP, PM, SJ, and vigilance were significantly higher after caffeine ingestion in comparison with placebo ingestion (p < 0.001). However, both simple and choice reaction times were significantly poorer during PSD in comparison with RN (p < 0.05 and p < 0.001, respectively). Therefore, ingesting caffeine is an effective strategy to maintain physical and cognitive performances after PSD.