Polypyrrole (PPy) nanoparticles have been synthesized successfully by oxidation polymerization in droplet microfluidic system. The resulting particles were characterized by Fourier-transform infrared spectroscopy, field emission scanning electron microscope, transition electron microscope, X-ray diffraction, thermal gravimetric analysis, and cyclic voltammetry. The in-channel synthesized nanoparticles are compared with those of PPy synthesized via conventional discontinuous batch reactor. The in-channel synthesis method leads to PPy nanoparticles that are different in properties such as improved conductivity over the regularly synthesized PPy. In comparison, the method is a fast, continuous and efficient method for PPy synthesis.