Modeling the effects of humidity and temperature gradients on the structural behavior of masonry walls reinforced with fiber reinforced polymer (FRP) composite is of great importance. Study of interfacial stresses, in particular, is a key factor in predicting the durability of the bond between the reinforcing FRP laminate and the host masonry. In this paper, a finite element modeling procedure for analyzing the hygro-thermo-mechanical response of multi-layered structures constructed with distinctive permeable materials was developed by incorporating structural stress analysis into the coupled moisture/temperature finite element model based on the governing equations proposed by Phillips and De Vries. The hygro-thermo-mechanical finite element model was used to analyze the response of a concrete block reinforced with a unidirectional glass/epoxy FRP composite laminate. The results demonstrated that the effect of temperature gradient on the moisture distribution, i.e., heat-induced moisture movement, resulted in an accumulation of moisture at the interface, and induced interfacial stresses even in the absence of a moisture gradient. The presented finite element modeling procedure can be used to aid with the design of FRP/masonry structure or other similar structures for minimizing interfacial stresses induced due to the mismatch of moisture swelling and thermal expansion properties of the constituent materials.