Recent literature confirms the ergogenic effect of acute caffeine intake to increase muscle strength and power in men. However, the information about the effect of caffeine on muscle performance in women is uncertain and it is unknown whether its ergogenicity is similar during the menstrual cycle. The goal of this investigation was to assess the effect of acute caffeine intake on mean and peak velocity of half-squat exercise during three different phases of the menstrual cycle. Thirteen trained eumenorrheic athletes (age = 31 ± 6 years; body mass = 58.6 ± 7.8 kg) participated in a double-blind, crossover and randomized experimental trial. In the early follicular (EFP), late follicular (LFP) and mid luteal phases (MLP), participants either ingested a placebo (cellulose) or 3 mg/kg/bm of caffeine in an opaque and unidentifiable capsule. In each trial, participants performed a half-squat exercise at maximal velocity with loads equivalent to 20%, 40% 60% and 80% of one repetition maximum (1RM). In each load, mean and peak velocity were measured during the concentric phase of the exercise using a rotatory encoder. In comparison to the placebo, a two-way ANOVA showed that the ingestion of 3 mg/kg/bm of caffeine increased mean velocity at 60% 1RM in EFP (Δ = 1.4 ± 2.7%, p = 0.04; ES: 0.2 ± 0.2) and LFP (Δ = 5.0 ± 10.4%, p = 0.04; ES: 0.3 ± 0.4). No other statistical differences were found for the caffeine-placebo comparison for mean velocity, but caffeine induced an ergogenic effect of small magnitude in all of the menstrual cycle phases. These results suggest that the acute intake of 3 mg/kg/bm of caffeine induces a small effect to increase movement velocity during resistance exercise in eumenorrheic female athletes. The positive effect of caffeine was of similar magnitude in all the three phases of the menstrual cycle.