Highly active and stable PtRu nanocatalysts supported on carbon nanotubes were prepared by microwave-assisted ethanol reduction in an ethanol/water mixture (1:1 v/v). During the reduction process, the presence of water is necessary for fast and substantial metal ion reduction. The prepared catalysts were characterized with inductively coupled plasma (ICP-ES), TEM, XRD, and electrochemical techniques to investigate their structural properties and electrocatalytic activities. ICP analysis confirms the presence of Pt and Ru in the catalysts, whereas XRD and TEM analyses demonstrate the formation of nanoparticles in the Pt face-centered-cubic structure that have a narrow size distribution and are well dispersed on carbon nanotubes. Metal loading and Pt/Ru ratio are closer to the nominal values for catalysts prepared through microwave-assisted ethanol reduction than those for catalysts prepared by conventional ethanol reduction. Heat treatment at different temperatures from 200 to 800 °C in a reductive atmosphere has a beneficial effect on the electrocatalytic activity of the catalysts and their stabilities under electrochemical conditions. A heat treatment temperature of 600 °C was found to be optimum for the activity and stability of the catalysts and tolerance for CO poisoning, which is discussed in view of the structural properties of the nanocatalysts and the higher degree of alloying. Temperatures higher than 600 °C led to the aggregation of nanocatalysts and formation of larger particles.