Chlorogenic acids (CGAs) are found in abundance in coffee beans and have numerous health benefits. This study investigated the effect of CGAs extracted from coffee beans on fatigue and sleep in healthy participants. This crossover study involved 16 men (aged 30–54 years) who were daytime workers with weekends off work. The participants were randomized into two groups: One group was given a placebo beverage, and the other was given an active beverage containing 300 mg of CGAs. The test beverages were consumed for 13 days starting on a Sunday. The evaluation criteria were feelings of fatigue and sleep quality, sleep-related indices recorded by an activity meter, and biomarkers. Feelings of fatigue and sleep-related indices during the first (first half of week 1) and second (second half of week 2) halves of the consumption periods were compared. Within the first half of week 1, no differences in feelings of fatigue were observed between the groups. However, during the second half of week 2, fatigue upon awakening and sleep quality in the active group were significantly improved compared with those in the placebo group. Sleep efficiency and total nocturnal awakening time were significantly deteriorated in the second half of week 2 compared with the first half of week 1 in the placebo group. Furthermore, significant differences in these indices were observed between the two groups in the second half of week 2. These results suggest that the daily consumption of CGA-containing beverages may improve fatigue upon awakening and sleep quality.