Fire is a significant threat to human lives and the integrity of buildings. To better understand the complex behavior of masonry exposed to high temperatures, thermal analyses were carried out to evaluate the temperature distribution in concrete blocks and stack-bond prisms exposed to high temperature levels. The effects of distinct specimen boundary conditions (restrict or easy access to air circulation inside the voids of the block and prisms) on the thermal response of the masonry materials were investigated. Thersys 2.0 software was used to implement three-dimensional thermal analysis of distinct finite element models. Four-node tetrahedral elements and full integration were used in all models. The modeling approach was validated by experimental data obtained from thermocouples embedded into masonry components. The results indicated that the boundary conditions significantly affected the time required for homogenization of temperature in blocks and prisms. Easy access to air circulation inside the voids of the prisms provided a faster temperature homogenization. In this scenario, the prism reached temperature ranges of (300 ± 0.5% × 300) °C and (600 ± 0.5% × 600) °C after exposure times of 2 h and 2 h 10 min, respectively. When access to air circulation within the voids of the prisms was limited, the same temperature ranges were achieved after exposure times of 5 h 20 min and 6 h, respectively.