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Background: As a systematic fungicide, prochloraz is often used to control banana freckle disease, and it is significant to assess the safety and risk of prochloraz. Methods: The dissipation kinetics and distribution of prochloraz in bananas were measured by high-performance liquid chromatography (HPLC). Results: The results showed that the fortified recoveries in bananas were 83.01–99.12%, and the relative standard deviations (RSDs) were 2.45–7.84%. The half-life of prochloraz in banana peel (3.93–5.60 d) was significantly lower than it was in whole banana (8.25–10.80 d) and banana pulp (10.35–12.84 d). The terminal residue of prochloraz in banana fruits was below the maximum residue level (MRL, China) at pre-harvest intervals (PHI) of 21 d. Moreover, the residue of prochloraz in banana peel was always 1.06–7.71 times greater than it was in banana pulp. The dietary risk assessment results indicated that the prochloraz residue in bananas at PHI of 21 d was safe for representative populations. (4) Conclusions: We found that a 26.7% prochloraz emulsion oil in water (EW) diluted 1000-fold and sprayed three times under field conditions was safe and reliable, providing a reference for the safe application of prochloraz in bananas.