In this work, an electrochemical methodology consisting of electrodeposition in ionic liquid-in water (IL/W) microemulsions has been revealed as an excellent pathway to prepare highly mesoporous nanorods with pore sizes of a few nanometers, with a significant growth rate. The nanochannels of a polycarbonate membrane (hard template) define the diameter of the nanorods, the deposited charge controls its length and the mesoporous structure replicates the structure of the microemulsion (soft template). This procedure has been used to prepare mesoporous nanorods of pure metal (Pt) or of alloy (CoPt3) with very high electrochemically active surface area (228 and 235 m2 g-1, respectively), as a consequence of the accessible three-dimensional interconnected network formed by the mesopores. When the synthesised mesoporous nanorods were tested as catalysts for ethanol electrooxidation in alkaline medium, excellent catalytic performance was found, with significant improvements over the performance of compact nanorods or commercial PtRu nanoparticles. The oxidation current / mass ratio of the mesoporous nanorod catalyst is significantly higher and, moreover, the onset potential of the ethanol oxidation is clearly advanced. Mesoporous CoPt3 nanorods show similar performance with pure platinum mesoporous nanorods and good stability in the alkaline medium, which makes them very good candidates as catalysts of the anodic reaction in direct ethanol fuel cells, with greater economy with respect to pure Pt catalysts.