In this work, a sub-minute and sensitive capillary electrophoresis with laser-induced fluorescence (CE-LIF) method was developed for the analysis and quantitation of the neurotransmitter 5-hydroxytryptamine (5-HT) or serotonin in urine. The method involves precolumn derivatization with fluorescein isothiocyanate isomer I (FITC) using an excitation light from an argon ion laser of 488 nm and a 520 nm band pass emission filter. Different variables that affect derivatization (pH, FITC concentration, reaction time and temperature) and separation (buffer concentration, pH, applied voltage and injection time) were studied. The linear dynamic range obtained was between 0 and 188 nM with a detection limit of 16 nm with a RSD between 2 and 9%. The applicability of the proposed method was demonstrated by analysis of 5-HT in human urine, establishing a concentration of 57 nM in control urine. The method was validated by standard-addition methodology.