A simple and validated micellar electrokinetic chromatographic method is described for the determination of 5-hydroxymethylfurfural (HMF). The method was applied to fresh and processed (heated at 65 °C, 85 °C and 105 °C for 5 h and 20 h) multifloral and honeydew honeys. Optimum conditions were: 10 mmol L−1 Tris buffer consisting 110 mmol L−1 SDS and 10% (v/v) MeOH at pH 9.10, 20 kV of applied potential, 3 s of injection time at 5 × 103 N m−2, 280 nm of wavelength and 25 °C of fixed temperature. Mean electrophoretic mobility (m2 s−1 V−1) of HMF and methyl paraben (IS) were − 5.28 × 10−5 (RSD of 0.745%) and − 2.52 × 10−4 (RSD of 0.944%), respectively. The calibration curve was linear in the range of 0.68 µg mL−1 (5.40 × 10−6 mol L−1) and 4.05 µg mL−1 (3.21 × 10−5 mol L−1) with R = 0.9990 for inter-day precision. LOD and LOQ values were 0.007 µg mL−1 (5.48 × 10−8 mol L−1) and 0.023 µg mL−1 (1.83 × 10−7 mol L−1), respectively, as inter-day precision. The accuracy was very high with recovery values between 94.07 and 97.16%. The developed method was fully validated according to ICH guidelines. The results were compared with those of HPLC method adapted from AOAC method no: 980.23.