The effects of temperature and pretreatment on drying kinetics and thermal degradation of phytonutrients present in pomegranate arils were investigated. The arils were divided into two groups, and half of the samples were pretreated by dipping into 80 °C hot water for 2 min. The drying process was conducted in the vacuum drier at the temperatures of 55, 65 and 75 °C. The fastest drying was completed at 75 °C after pretreatment of the samples. The highest anthocyanin–phenolic compound contents and antioxidant capacity were detected in the arils dried at 55 °C. Seven thin-layer drying models were used to predict drying curves, and Arrhenius and Eyring–Polanyi models were employed to predict phytonutrient degradation kinetics. Activation energy for drying was 24.26 kJ mol−1 for pretreated samples and 31.54 kJ mol−1 for untreated samples. Effective moisture diffusivities were ranged from 1.43 × 10−9 to 6.03 × 10−9 m2 s−1.