In the present study, a novel and eco-friendly vortex-assisted ionic liquid-based microextraction method was developed for the determination of selenium in food. The microextraction method is based on the liberation of iodine in the presence of selenium; the liberated iodine reacts with I− to form I3−. Anionic I3− reacts with cationic crystal violet dye, and the product is extracted into 1-hexyl-3-methylimidazolium hexafluorophosphate phase in the presence of Triton X-114. The proposed method is linear in the range of 2.0–70µgL−1 and has a detection limit of 9.8×10−2µgL−1. Relative standard deviations were 3.67% and 2.89% for the five replicate measurements of 14 and 35µgL−1 Se(IV), respectively. The proposed method was successfully applied to different food samples (NIST SRM 2976 mussel tissue, pepper, ginger, wheat flour, red lentil, traditional soup, cornflour, cornstarch, and garlic) after microwave digestion.