Oxygen invasion is the main bottleneck in developing microscale microbial fuel cells as an efficient power source. This study reports for the first time the development of a polydimethylsiloxane-based co-laminar microbial fuel cell utilizing a parylene C coating to lower the oxygen permeability. In addition, the surface of the Au electrode is micropillar-structured to reduce the internal resistance of the microbial fuel cell. The performance of this novel microfluidic microbial fuel cell is investigated under various flow rates of electrolytes. The shear stress simulation shows that shear stress, induced by increasing flow rates, strongly impacts the biofilm electrode performance. To the best of our knowledge, the measured peak power density (71.89 +/- 5.13 mu W cm(-2)) and maximum current density (182.0 +/- 4.82 mu A cm(-2)) with the structured electrode are higher than those of any other reported polydimethylsiloxane-based microscale microbial fuel cells. The proposed microbial fuel cell appears to be a promising power supply that can be easily integrated with portable or implantable biomedical devices.