Microfluidic direct methanol fuel cell (DMFC) has some key issues, such as fuel crossover and water management, which typically hamper the development of conventional polymer electrolyte-based fuel cells. Here a method of minimizing fuel crossover in microfluidic DMFC is reported. A polymer separator at the interface of the fuel and electrolyte streams in a single-channel microfluidic DMFC is used to reduce the cross-sectional area across where methanol can diffuse. Based on the optimized fuel rate, fuel concentration and pore radius, a maximum power density of 7.4mWcm(-2) was obtained with the separator using 2M methanol. This simple design improvement reduces the voltage loss at the cathode and leads to better performance. Copyright (c) 2014 John Wiley & Sons, Ltd.