Induced resistance is an alternative disease control strategy for postharvest fruits and vegetables. Methyl jasmonate (MeJA) is a crucial phytohormone in the defense response to biotic and abiotic stresses. The effect and relevant mechanism of MeJA on the control of postharvest disease in mango fruit remain unclear. This study investigated the effect and possible mechanism of MeJA against stem-end rot caused by Lasiodiplodia theobromae in mango fruit. The results showed that MeJA significantly inhibited the lesion expansion on mango fruit inoculated with L. theobromae. 10 μM MeJA treatment effectively induced disease resistance against L. theobromae during postharvest storage. MeJA enhanced the activities of defense-related enzymes, including phenylalanine ammonia lyase (PAL), peroxidase (POD), β-1,3-glucanase (GLU), and chitinase (CHT), increased the accumulation of endogenous jasmonic acid (JA) and salicylic acid (SA) contents, up-regulated the expressions of the related genes on JA pathway (AOS, JAR1, MYC2, and COI1) and SA pathway (ICS, and PR1), stimulated the contents of total phenolics and flavonoids, and inhibited the accumulation of malondialdehyde (MDA). Furthermore, MeJA delayed the ripening and senescence of the fruit by inhibiting the peel yellowing, flesh softening and change in soluble solids content (SSC) of mango fruit. The results indicated that the enhanced resistance of MeJA-treated mango to stem-end rot was potentially due to the activation of defense responses induced by synergistic interaction between JA and SA pathways, as well as delayed postharvest ripening. The MeJA treatment is a promising strategy to control stem-end rot of mango fruit.