This paper reports on a study to determine the structural dynamic characteristics, such as natural frequencies, mode shapes and damping ratios, of timber mosques using ambient vibration tests after restoration. Kusluca historical timber mosque in the Surmene district of Trabzon, Turkey is selected as a case study. The mosque was built in the early twentieth century with two floors. Restoration projects were prepared in 2008 and the mosque was re-opened in 2011. A finite-element model of the mosque was constituted based on restoration drawings, and modal analysis was performed using orthotropic material properties. A literature review was used to determine the initial dynamic characteristics, such as natural frequencies, mode shapes and damping ratios. Non-destructive experimental measurements were conducted after construction to validate the numerical results using in situ tests. The first three natural frequencies were obtained numerically and experimentally. There was a close agreement between mode shapes, but 30% difference in natural frequencies. To minimise the differences, the finite-element model was updated using manual and automated updating procedures, changing uncertain parameters such as material properties, semirigid element connections, boundary conditions and section properties.