While previous studies have explored a range of factors governing the optimal use of caffeine (CAF) in athletes, limited research has explored how time of day (TOD) affects the ergogenic effects of various CAF dosages on physical performance. This study aimed to increase knowledge about how different recommended CAF doses (3 mg/kg vs. 6 mg/kg) ingested at different TODs affected maximal high-intensity physical performance and the perception of potential side effects in female athletes. In this double-blind, randomized, and counterbalanced study, 15 low CAF consumer athletes (aged 18.3 ± 0.5 y) underwent six trials, including three testing conditions assessed across two TODs: one in the morning (08:00 a.m.) and one in the evening (06:00 p.m.). During each condition, the participants ingested either a placebo, 3 mg/kg CAF (CAF (3 mg)), or 6 mg/kg CAF (CAF (6 mg)) capsules 60 min before each test with an in-between washout period of at least 72 h. In each trial, the participants performed a countermovement jumps test (CMJ), a modified agility t test (MATT), a repeated sprint ability (RSA), a rating of perceived exertion (RPE), and finally, a CAF side effects questionnaire. Our findings indicate the absence of an ergogenic effect on CMJ, MAT, and RSA performance in the evening after administering CAF (3 mg) or CAF (6 mg) compared to a placebo. Likewise, when CAF was ingested in the morning, there was an improvement in these performances with both CAF (3 mg) and CAF (6 mg), with greater improvement observed after CAF (6 mg). Additionally, neither the CAF dosage nor the TOD had a significant effect on the RPE. The occurrence of side effects increased significantly after the evening ingestion of CAF, particularly with a moderate dose of CAF (6 mg). Our findings indicate that the effectiveness of CAF depends on the TOD and CAF dosage. When ingested in the morning, a moderate dose of CAF (6 mg), rather than CAF (3 mg), is more effective in improving short-term physical performance without affecting CAF side effects in female athletes. Nevertheless, when ingested in the evening, neither dose was sufficient to enhance short-term physical performance, and both dosages increased the incidence of CAF side effects, particularly at a moderate dose.