Physicochemical stability and thermal degradation of vitamin E (VE) in nanoemulsions fabricated by low energy emulsification method known as Emulsion Phase Inversion: catastrophic phase inversion (EPI) with different carrier oils (short-chain, medium-chain and long-chain triglycerides) and Tween 80 were investigated. Although nanoemulsions made with VE and the 3 carrier oils showed physical stability to heat shock (30–90 °C, 30 min), ionic strength (0–500 mM), pH (2.0–8.5) and long term storage (60 days, under light and darkness, 4, 25 and 40 °C), there was significant VE degradation in heat processed and long-term storage samples. The VE degradation in long-term storage fitted well with Weibull model, while heat degradation followed the first order kinetics, with medium-chain triglyceride (MCT) based nanoemulsions held at 90 °C showing the greatest degradation rate (k = 0.1526 × 10−3 min−1) and lowest half-life of 4.54 min. The lack of droplets aggregation or coalescence was associated with absence of electrostatic screening and ion-binding effects. The nanoemulsions stored at 4 °C were more stable than those at 40 °C. The short-chain triglyceride (SCT) based nanoemulsions did not physically withstand the high temperatures (>25 °C) while long-chain triglyceride (LCT) showed good retention in all studied conditions. The VE retention was increased when nanoemulsions were stored in the dark. This study might be helpful to food and pharmaceutical industries in choosing better processing and storage conditions of VE delivery systems.