A microemulsion electrokinetic chromatography (MEECK) method for patulin (PAT) quantification in apple juice samples has been developed. The effects of several important factors such as co-surfactant type, concentration of surfactant, acetonitrile percentage in the microemulsion, and running voltage and temperature were investigated to determine the optimum conditions. They resulted to be: a background electrolyte (BGE) composed of 25 mM of sodium tetraborate, SDS (2.16% w/w), ethanol (6.49% w/w), n -octanol (0.82% w/w) and 2% v/v acetonitrile; applied voltage of +15 kV; and a capillary temperature of 35 °C. PAT was detected at 276 nm. Quantification and detection limits (LOQ and LOD) in apple juice samples were 8.0 μg L −1 and 3.2 μg L −1 , respectively. Patulin was extracted from apple juice using ethyl acetate with a mean recovery value of 75.3% (RSD = 4.5). This method was applied to the measurement of patulin in twenty commercial apple juice samples obtained from different Danish supermarkets. The PAT apple juice mean and median levels obtained were 35.9 and 10.9 μg L −1 , respectively. The comparison with a previously validated micellar electrokinetic chromatography (MEKC) method for PAT analysis showed the suitability of using MEEKC for this mycotoxin analysis. However, the expectations of obtaining a higher efficiency and thus lower limits of detection and quantitation when using MEEKC were not met.