Background: Preexercise caffeine intake has proven to exert ergogenic effects on cycling performance. However, whether these benefits are also observed under fatigue conditions remains largely unexplored. We aimed to assess the effect of caffeine ingested during prolonged cycling on subsequent time-trial performance in trained cyclists. Methods: The study followed a triple-blinded, randomized, placebo-controlled cross-over design. Eleven well-trained junior cyclists (17 ± 1 years) performed a field-based 8-min time trial under “fresh” conditions (i.e., after their usual warm-up) or after two work-matched steady-state cycling sessions (total energy expenditure∼20 kJ/kg and ∼100 min duration). During the latter sessions, participants consumed caffeine (3 mg/kg) or a placebo ∼60 min before the time trial. We assessed power output, heart rate, and rating of perceived exertion during the time trial and mood state (Brunel Mood Scale) before and after each session. Results: No significant condition effect was found for the mean power output attained during the time trial (365 ± 25, 369 ± 31, and 364 32 W for “fresh,” caffeine, and placebo condition, respectively; p = .669). Similar results were found for the mean heart rate (p = .100) and rating of perceived exertion (p = 1.000) during the time trial and for the different mood domains (all p > .1). Conclusions: Caffeine intake during prolonged exercise seems to exert no ergogenic effects on subsequent time-trial performance in junior cyclists. Future studies should determine whether significant effects can be found with larger caffeine doses or after greater fatigue levels.