Novel methods were developed for the specific entrapment and separation of phosphorylated compounds using Phos-tag polyacrylamide gels fabricated at the channel crossing points of the microfluidic electrophoresis chips. The channel intersection of the microchip was filled with a solution comprising acrylamide, N,N-methylene-bisacrylamide, Phos-tag acrylamide, and 2,2'-azobis [2-methyl-N-(2-hydroxyethyl)propionamide], which functioned as a photocatalytic initiator. In situ polymerization at the channel crossing point was performed by irradiation with a UV LED laser beam. The electrophoretically trapped phosphorylated compounds were released from the gel by switching the voltage to deliver high concentrations of phosphate and EDTA in a background electrolyte and fluorometrically detected at the end of the separation channel. Under the optimized conditions, the phosphorylated compounds were concentrated by a factor of 100-fold, and the peak resolution was comparable to that obtained by pinched injection that a common microchip electrophoresis analysis method. This method was successfully utilized to preconcentrate and analyze phosphorylated peptides.