A micellar electrokinetic chromatography method has been developed for simultaneous determination of melatonin and its precursors and metabolites. A 20 mM borate buffer pH 9.5 with 50 mM SDS served as the electrolyte. Tryptophan, 5-methoxyindoleacetic acid, 6-hydroxymelatonin, melatonin, serotonin, and 5-methoxytryptamine were baseline separated in less than 13 min. The limits of detection for UV detection and fluorometric detection based on native fluorescence of analytes were at the sub-ppm level. The proposed method with UV detection was applied to melatonin content control in pharmaceutical tablets with a precision expressed as RSD (n = 7) = 1.6%. For biological samples extraction with chloroform and ethyl acetate was examined. With ethyl acetate and chloroform recoveries of 87.2% and 82.1% melatonin, respectively, were obtained from plasma samples. The recovery of melatonin from spiked urine samples was 80.0% for ethyl acetate and 82.5% for chloroform. Fluorometric detection provides about two-fold improvement over UV in the detection of melatonin and minor improvements for three other analytes, but is much poorer than UV for tryptophan and 6-hydroxymelatonin in applied conditions.