The effect of the synthesis procedure of SBA-15 on its catalytic behavior in methane decomposition (DeCH4) for hydrogen production has been investigated. Three different SBA-15 materials have been synthesized: SBA-15 (C), by a conventional method with a final calcination step; SBA-15 (MW), replacing the calcination by microwave digestion; and SBA-15 (ULP), using a micelle expander to generate ultra-large pores. All SBA-15 samples exhibit a reaction induction time necessary for the formation of Si–C linkages associated with the creation of active sites. After a sharp decay of the reaction rate due to the appearance of mass transfer limitations, all the SBA-15 materials reach a quasi-stationary state which is maintained during the rest of the reaction time tested (24 h). The long-term activity is mainly due to fact that the carbon deposits grow towards the outer part of the SBA-15 particles, keeping part of the active sites accessible to methane molecules. Among the materials tested, SBA-15 (C) exhibits the highest long-term activity and resistance to deactivation, mainly due to its higher thermal stability. Finally, the activation energy (217.8 ± 0.5 kJ mol−1) and reaction order (0.5) corresponding to SBA-15 (C) indicate that DeCH4 proceeds with crystallite growth as controlling process and a dissociative reaction mechanism.