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Historic Cairo has been a UNESCO World Heritage Site since 1979. It has more than 600 historic structures, which require extensive studies to sustain their cultural, religious, and economic values. The main aim of this paper is to undertake dynamic investigation tests for the dome of Fatima Khatun, a historic mausoleum in Historic Cairo dating back to the 13th century and consisting of mainly bricks and stones. The challenge was that the structure was difficult to access, and only a small portion of the top was accessible for the attachment of accelerometers. Current dynamic identification procedures typically adopt methods in which the sensors are arranged at optimal locations and permit direct assessment of the natural frequencies, mode shapes, and damping ratios of a structure. Approaches that allow for the evaluation of dynamic response for structures with limited accessibility are lacking. To this end, in addition to in situ dynamic investigation tests, a numerical model was created based on available architectural, structural, and material documentation to obtain detailed insight into the dominant modes of vibration. The free vibration analysis of the numerical model identified the dynamic properties of the structure using reasonable assumptions on boundary conditions. System identification, which was carried out using in situ dynamic investigation tests and input from modelling, captured three experimental natural frequencies of the structure with their mode shapes and damping ratios. The approach proposed in this study informs and directs structural restoration for the mausoleum and can be used for other heritage structures located in congested historic sites.