Crucial to the interpretation of the results of any finite element analysis of a skeletal system is a test of the validity of the results and an assessment of the sensitivity of the model parameters. We have therefore developed finite element models of two crania of Macaca fascicularis and investigated their sensitivity to variations in bone material properties, the zygomatico-temporal suture and the loading regimen applied to the zygomatic arch. Maximum principal strains were validated against data derived from ex vivo strain gauge experiments using non-physiological loads applied to the macaque zygomatic arch. Elastic properties of the zygomatic arch bone and the zygomaticotemporal suture obtained by nanoindentation resulted in a high degree of congruence between experimental and simulated strains. The findings also indicated that the presence of a zygomatico-temporal suture in the model produced strains more similar to experimental values than a completely separated or fused arch. Strains were distinctly higher when the load was applied through the modelled superficial masseter compared with loading an array of nodes on the arch. This study demonstrates the importance of the accurate selection of the material properties involved in predicting strains in a finite element model. Furthermore, our findings strongly highlight the influence of the presence of craniofacial sutures on strains experienced in the face. This has implications when investigating craniofacial growth and masticatory function but should generally be taken into account in functional analyses of the craniofacial system of both extant and extinct species.