Mosques are sanctuary places for Muslims where they can perform their religious activities and also can communicate with each other. On the other hand, historical mosques may contain artworks which have cultural heritage values. These mosques originally have not any Heating, Ventilating and Air-Conditioning systems. For this reason, obtaining thermal comfort becomes a significant issue. In this study, a systematic approach on monitoring and evaluating thermal comfort of historical mosques were developed. As a case study, The Ulu Mosque, Manisa/Turkey was monitored from 2015 to 2018, and thermal comfort evaluation of the mosque was conducted during prayer times based on the method provided by ISO 7730. A dynamic Building Energy Performance Software, DesignBuilder, was used to model the mosque, and the model was calibrated by using hourly indoor temperature data. The calibrated model was then used to evaluate existing conditions of the mosque and develop retrofitting scenarios in order to increase thermal comfort of prayers. Thirteen different scenarios were proposed to improve thermal comfort of prayers during worship periods. The results were evaluated according to EN 16883 for conservation of cultural heritage of the mosque. Electrical radiator heating with intermittent operating schedules was obtained as the best scenario to protect cultural heritage via artworks, while decreasing disssatisfaction level of the prayers from 45% to 10% in winter months. Additionally, intermittent operation saved 46.9% of energy compared to continuous operating schedule.