We report a method of reducing the spot size of an electron beam in a portable pyroelectric electron probe microanalyzer (EPMA) and its application to on-site microanalysis. An electron beam with a spot size of 40 μm full width at half maximum was achieved by preventing the production of an electric field on the side of a needle tip set on the pyroelectric crystal in the EPMA by coating the side of the tip with an insulating material. This spot size was approximately 10 times smaller than that previously reported. We were able to acquire a line scan profile of a thin copper line sputtered on a silicon substrate using the portable pyroelectric EPMA. The width of the sputtered copper evaluated from the line scan profile (120 μm) corresponded to that from a line scan profile obtained by conventional stationary scanning electron microscope-energy dispersive X-ray spectroscopy equipment.