The aim of this study was to develop a new and fast micellar electrokinetic chromatography (MEKC) method for the determination of phenylalanine in cereal samples. The background electrolyte was chosen by a factorial design and was composed of 30 mmol/L phosphoric acid, 100 mmol/L sodium dodecyl sulfate, and 25% methanol (v/v) at pH 1.9. A fused silica capillary (48.5 cm total length×8.5 cm effective length×50 μm id×375 μm od) was used in a short-end injection configuration, and direct UV detection was at 200 nm. The method was validated following the Eurachem guidelines, and values such as linearity (from 10.1 to 40.4 mg/L); recovery (86.8-103.9%); repeatability (0.06-0.22% for migration time and 1.14-4.82% for peak area); reproducibility (0.04-0.61% for migration time and 2.22-5.72% for peak area); and LOD and LOQ of 20 and 60 mg/100 g, respectively, were obtained. After the comparison involving selectivity and accuracy between capillary electrophoresis and LC/MS/MS method, the MEKC-UV method was successfully applied to analysis of phenylalanine in different cereal products.