The influence of catalyst pretreatment and space velocity in methane decomposition into COx-free hydrogen and carbon nanotubes were investigated over CoMo/MgO catalyst. The reduction of catalyst before methane decomposition leads to a hydrogen production without significant formation of COx (concentration lower than 5 ppm after 25 min of reaction) suitable for its use in fuel cells. However, a high hydrogen space velocity in the pretreatment increased the rate of catalyst deactivation. The CO and CO2 formation rates showed a common trend for all conditions tested: there was a high initial rate and, after 2 min of reaction, there was a lower stabilized rate. The increase in methane space velocity increased the hydrogen formation rate and the degree of carbon nanotubes graphitization. However, it strongly decreases methane conversion, as expected. The use of low hydrogen space velocity, 0.25 h−1, in catalyst pretreatment and high methane space velocity, 8 h−1, in reaction step, provided the highest hydrogen yield and well-structured carbon nanotubes.