Hadamard transform electrophoresis combined with laser-induced fluorescence (LIF) detection on a microchip was demonstrated. A compact, diode-pumped neodymium-doped yttrium aluminum garnet laser was employed as the light source for LIF detection. The analytical conditions were optimized using rhodamine B as the analyte. Under optimal conditions, the signal-to-noise ratio (S/N) of the analyte was improved by a factor of 7.5 by means of Hadamard transformation based on a 255-order cyclic S matrix. Additionally, the relationship between fluorescence intensity and analyte concentration was linear with a correlation coefficient of 0.993 in the inverse Hadamard transformed data at the concentration range from 25 to 100 pM. The results indicate that the present method is applicable to quantitative analysis at the concentration lower than the concentration limit of detection in a conventional method. The concentration limit of detection was ∼25 pM (the relative standard deviation of the peak height was 5.2%). The present technique was successfully applied to the separation of a mixture containing 1.9 nM phenylalanine and 1.9 nM glutamic acid labeled with rhodamine B isothiocyanate. The S/Ns of the analyte peaks were improved up to ∼10 in the inverse Hadamard transformed data derived from a 127-order cyclic S matrix, while neither peak was lower than the limit of detection (S/N≪3) in conventional microchip electrophoresis by a single injection.