Hydrogen is seen as the new energy carrier for sustainable energy systems of the future. Meanwhile, proton exchange membrane fuel cell (PEMFC) stacks are considered the most promising alternative to the internal combustion engines for a number of transportation applications. Nevertheless, PEMFCs need high-grade hydrogen, which is difficultly stored and transported. To solve these issues, generating hydrogen using membrane reactor (MR) systems has gained great attention. In recent years, the role of silica membranes and MRs for hydrogen production and separation attracted particular interest, and a consistent literature is addressed in this field. Although most of the scientific publications focus on silica MRs from an experimental point of view, this review describes the progress done in the last two decades in terms of the theoretical approach to simulate silica MR performances in the field of hydrogen generation. Furthermore, future trends and current challenges about silica membrane and MR applications are also discussed.