A new micellar electrokinetic capillary chromatography (MEKC) method combined with field-amplified sample injection (FASI) has been developed for the analysis of isonicotinamide and nicotinamide in whitening cosmetics and supplemented foodstuffs. Parameters affecting FASI preconcentration and MEKC separation were optimized systematically. Compared with direct MEKC, the sensitivity of FASI-MEKC was improved by 12.8- and 9.8-fold for isonicotinamide and nicotinamide, respectively. The detection limits (LODs) of isonicotinamide and nicotinamide were 0.051 μg mL⁻¹ and 0.069 μg mL⁻¹, respectively, with RSD (intraday) < 4.9% (n = 7, c = 0.5 μg mL⁻¹) and RSD (interday) < 6.4% (n = 5, c = 0.5 μg mL⁻¹). The proposed method was successfully applied in determination of isonicotinamide and nicotinamide in whitening cosmetics and supplemented foodstuffs with acceptable recoveries of 84.7–108.4%.