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ε-poly-<span style="font-variant: small-caps;">l</span>-lysine (ε-PL) holds a strong antibacterial property and is widely used for food preservation. However, the application of ε-PL to enhance fruit disease resistance in postharvest longans (<i>Dimocarpus longan</i> Lour.) has not been explored. The objective of this study was to explore the impact of ε-PL treatment on disease occurrence and energy metabolism of longans infected with <i>Phomopsis longanae</i> Chi (<i>P</i>. <i>longanae</i>). It was found that, in comparison with <i>P</i>. <i>longanae</i>-inoculated longans, ε-PL could decrease the fruit disease index and adenosine monophosphate (AMP) content, increase the amounts of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and energy charge, and enhance the activities of adenosine triphosphatase (ATPase) (such as H⁺-, Mg²⁺-, and Ca²⁺-ATPase) in the mitochondria, protoplasm, and vacuole. The results suggest that the higher levels of ATPase activity and energy status played essential roles in disease resistance of postharvest longan fruit. Therefore, the ε-PL treatment can be used as a safe and efficient postharvest method to inhibit the disease occurrence of longan fruit during storage at room temperature.