Abstract Background Enzymatic browning and microbial decay are the primary concerns that limit the postharvest life of longan fruit. These factors can be effectively prevented by sulfur dioxide (SO₂) fumigation; however, due to the safety and regulatory issues of SO₂, other alternatives must be tested. In this study, antioxidant and antimicrobial activities of thymol were determined against the pericarp browning and decay of longan fruit. A simple, cost-effective method was designed for its controlled release. Thymol vapors were obtained from the slurry prepared from 5 g of thymol in 5 mL of distilled water in a 180-mL glass jar, hermetically sealed and allowed for 24 h to accumulate the vapors in the headspace. Fruits were packed in polyethylene packages and fumigated with thymol through a septum. Non-fumigated fruits served as control and all the packages were stored at 25 ± 2 °C for 8 days. Results Thymol significantly (P ≤ 0.05) retarded pericarp browning (BI), delayed the decay incidence (DI) and maintained high color values of longan pericarp. Thymol also retained high total phenolic (TPC) and total flavonoid (TFC) contents, inhibited polyphenol oxidase (PPO) and peroxidase (POD) activities than those in control. A high coefficient of correlation of PPO with BI (r = 0.86), L* (r = − 0.94), weight loss (r = 0.93), TPC (r = − 0.77), TFC (r = − 0.80), DI (r = 0.92) and many other quality and color parameters indicated the antioxidant efficacy of thymol. Longer shelf life of 8 days with good quality attributes was obtained in thymol-treated fruits than 6 days in control. Conclusion Thymol could be effectively used as a natural antioxidant for a wide range of fruits. Graphic abstract