This study evaluated the efficacy of chitosan (CH) functionalized with 24-epibrassinolide (EBR) coating in terms of preserving the postharvest quality of late-harvested pomegranate (cv. Wonderful) fruit. Late-harvested pomegranate fruit were immersed for 3 min in different surface treatment solutions—CH 1.5% (w/v), CH + 2 µM EBR, CH + 5 µM EBR, CH + 10 µM EBR and CH + 15 µM EBR—and distilled water was used as a control treatment. The fruit were air-dried and subjected to long storage duration at 5 °C with 85 ± 5 RH for 12 weeks. At 4-week sampling intervals, a batch of fruits was placed at 21 ± 2 °C and 65–70% RH for a further 3 d period to simulate retail conditions before measurements were taken. Fruit physiological responses, physico-chemical properties, phytochemical contents, antioxidant capacity and physiological disorders were monitored during storage. The results showed that the CH-EBR composite edible coatings significantly (p < 0.05) delayed degradative processes due to senescence. The CH-EBR treatments delayed colour, texture and total soluble solids (TSS) degradation and reduced weight loss, respiration, electrolyte leakage and spoilage compared to the control and CH treatment. The treatment effect was more noticeable on fruit treated with CH + 10 µM EBR, which exhibited lower weight loss (18.19%), respiration rate (7.72 mL CO2 kg−1 h−1), electrolyte leakage (27.54%) and decay (12.5%), and maintained higher texture (10.8 N) and TSS (17.67 °Brix) compared to the untreated fruit with respective values of 24.32%, 18.06 mL CO2 kg−1 h−1, 43.15%, 37.5%, 8.32 N and 17.03 °Brix. This was largely attributed to the significantly higher antioxidant content, including the ascorbic acid content, total phenol content, total anthocyanin content and DPPH (radical scavenging activity), of the coated fruit compared to the control fruit. Therefore, CH + 10 µM EBR treatment is recommended as a postharvest management strategy to improve the quality preservation of late-harvested pomegranate fruit during storage.