Eleven alkaloids (1–11) including seven new ones, 1–7, were isolated from the solid fermentation of Aspergillus fumigatusVDL36, an endophytic fungus isolated from the leaves of Vaccinium dunalianumWight (Ericaceae), a perennial evergreen shrub distributed across the Southwest regions of China, Myanmar, and Vietnam. Their structures were elucidated on the basis of extensive spectroscopic methods. The isolates were evaluated for in vitroantifungal activities against five phytopathogenic fungi (Fusarium oxysporum, Coriolus versicolor, Fusarium solani, Botrytis cinerea, Fusarium graminearum). As a result, the new compounds fumigaclavine I (1), 13-ethoxycyclotryprostatin A (5), 13-dehydroxycyclotryprostatin A (6), and 12β-hydroxy-13-oxofumitremorgin C (7) exhibited antifungal activities with MIC values of 7.8–62.5 μg/mL which were comparable to the two positive controls ketoconazole (MIC = 7.8–31.25 μg/mL) and carbendazim (MIC = 1.95–7.8 μg/mL). Furthermore, compounds 1and 5demonstrated potent protective and curative effects against the tomato gray mold in vivo. Preliminary structure–activity relationships of the tested indole diketopiperazine alkaloids indicate that the introduction of a substituent group at position C-13 enhances their biological activities.