The present paper showcases the work carried out as part of the seismic retrofit of the Ottoman fortress of Gjirokastra, a UNESCO World Heritage site located in Albania. The need for strengthening and retrofitting the structure stems from the fact that it is situated in a region of high seismicity and showed signs of structural distress at the time of investigation. The hill on which the castle is built also has stability issues. The seismic retrofit focused on a damaged stone masonry tower of the fortress and was designed following a comprehensive methodology for the inspection, diagnosis and geotechnical and structural analyses. Through the use of non-destructive tests, the existing soil conditions, the material properties and composition and the dynamic behaviour of the tower were assessed. Nonlinear finite element analysis was used to establish the cause of the existing damage and to determine the most effective strengthening solutions. The findings of the investigation revealed potential causes of the observed damage as well as the need to carry out retrofitting works at the tower beyond ground improvement solutions to bring the performance of the structure up to the code-specified level. This paper highlights the importance of planning and coordination between all the relevant disciplines involved in the project, so that apt inspection and diagnostic tools can be used to fill in the gaps where information is missing and to design optimal and integrated structural interventions in historic structures. Satisfactory seismic performance can be obtained by using a combination of retrofitting techniques, which specifically target the weak elements identified via the analyses.