A novel design of a silicon-based micro-reformer for onboard hydrogen generation from ethanol is presented in this work. The micro-reactor is fully fabricated with mainstream MEMS technology and consists of an active low-thermal-mass structure suspended by an insulating membrane. The suspended structure includes an embedded resistive metal heater and an array of ca. 20k vertically aligned through-silicon micro-channels per square centimetre. Each micro-channel is 500 μm in length and 50 μm in diameter allowing a unique micro-reformer configuration that presents a total surface per projected area of 16 cm2 cm−2 and per volume of 320 cm2 cm−3. The walls of the micro-channels become the active surface of the micro-reformer when coated with a homogenous thin film of Rh–Pd/CeO2 catalyst. The steam reforming of ethanol under controlled temperature conditions (using the embedded heater) and using the micro-reformer as a standalone device are evaluated. Fuel conversion rates above 94% and hydrogen selectivity values of ca. 70% were obtained when using operation conditions suitable for application in micro-solid oxide fuel cells (micro-SOFCs), i.e. 750 °C and fuel flows of 0.02 mlL min−1 (enough to feed a one watt power source).