A case study was conducted to investigate the applicability of the equivalent frame modelling for the nonlinear time-history analysis of unreinforced masonry buildings with flexible diaphragms. The dynamic responses calculated from the equivalent frame models were compared against shake table test results of a full-scale two-storey stone masonry building. The investigated modelling approach reflected the simplifications commonly assumed for the global analysis of buildings; namely, considering the diaphragms to behave elastically and neglecting the stiffness and strength contributions of the out-of-plane responding walls. The sensitivity of the analysis to different idealisations of the equivalent frame, as well as to the diaphragm stiffness values, were also investigated. Discussions are provided on the accuracies and limitations of the investigated modelling approach, which may serve as a useful guidance for practical application.