Sulphur dioxide has been used to control pericarp browning in longan fruit. However, due to health and regulatory concerns, alternative treatments should be tested. The objective of this study was to find the tolerance levels of longan fruit to low O2 (2%, 5%, 10% and 15%) and elevated CO2 (5%, 10%, 15% and 20%) at 2 °C. According to the tolerance study, controlled atmospheres (CA) of 5% O2 + 5% CO2, 5% O2 + 10% CO2 and 5% O2 + 15% CO2 were compared with normal air (control) at 2 °C. Pericarp browning and decay incidence of longan were significantly (P ≤ 0.05) higher in control than all the CA treatments. CA storage reduced polyphenol oxidase (PPO) activity, maintained L* value and slowed down a decrease in total phenolic contents (TPC). Pericarp browning was highly correlated with PPO, L* and TPC.