This paper reports the results obtained for microwave-assisted catalytic fast pyrolysis (MACFP) of rice husk. The MACFP process employed a hierarchical catalyst prepared via a combination of organic alkali treatment (TPAOH) and the generation of an external layer of MCM-41-type mesoporous channels. We propose this catalyst which is used for the first time for pyrolysis of lignocellulosic biomass, as a tool to reduce coke agglomeration and increase hydrocarbon yields. Our results indicate that during catalyst preparation the mass fraction of cetyltrimethylammonium bromide (CTAB) has a direct effect on the content of MCM-41 formed on top of the HZSM-5 core. For MACFP, we hypothesize that the small molecules generated from thermal decomposition of rice husk react further to form aromatic and aliphatic hydrocarbons by decarbonylation, decarboxylation, oligomerization and aromatization. The highest hydrocarbon yield (60.5%) was obtained for a catalyst modified by a 2.0 mol/L TPAOH solution, with 10 wt% of CTAB (template for producing MCM-41), as well as with digestion and crystallization at 110 °C for 24 h. In addition, the highest liquid yield (47.6 wt%) was obtained at 550 °C. The relative content of hydrocarbons goes through a maximum of 60.5% with CTAB mass fraction which was higher than values obtained with MCM-41 (3.2%) and HZSM-5 (36.0%). Characterization and catalytic testing results suggest that the digestion temperature plays a more important role in the catalyst synthesis than the crystallization temperature. High digestion temperature (120 °C) decreases the overall hydrocarbon selectivity from 60.5% (110 °C) to 39.2%. The relative content of oxygenates reached the lowest value of 35.9% at the digestion and crystallization temperature of 110 °C. The synergistic effect of the MCM-41 shell and the HZSM-5 core promotes the catalytic activity, leading to outstanding deoxygenation capabilities and excellent selectivity to BTEX (52.7%).