Harvested longan fruit is prone to endocarp browning, which restricts preservation quality and shelf life. The antioxidant system defends against oxidative stress-mediated quality deterioration such as fruit browning. The study aimed to evaluate the effect of tert-Butylhydroquinone (TBHQ) on anti-browning ability of longan fruit in association with antioxidant capacity. The results indicated that application of 0.02% TBHQ significantly suppressed the progression of endocarp browning. In comparison with control, TBHQ treatment decreased the levels of hydrogen peroxide (H2O2), superoxide radical (O2−⋅), and malondialdehyde (MDA), and retained high levels of ascorbic acid (AsA), glutathione (GSH), total phenolics as well as 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging rate. Enhanced enzymatic activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione reductase (GR), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), but inhibited polyphenol oxidase (PPO) and peroxidase (POD) activities were also observed in TBHQ-treated fruit. Gene expression analysis suggested oxidative stress-related genes including DlSOD, DlCAT, DlGR, and DlAPX were up-regulated after TBHQ treatment. The results suggest that TBHQ is effective in alleviating endocarp browning by increasing antioxidant capacity of longan fruit.