A novel method to derive surface temperatures from aerial thermography is proposed. Its theoretical foundation, details regarding the implementation, relevant sensitivities, and its application on a day and night survey are presented here. The method differs from existing approaches particularly in two aspects: first, a three-dimensional sampling approach is used to determine the reflected thermal radiation component. Different surface classes based on hyperspectral classification with specific properties regarding the reflection and emission of thermal radiation are considered in this sampling process. Second, the method relies on a detailed, altitude-dependent, directionally and spectrally resolved modelling of the atmospheric radiation transfer and considers the spectral sensitivity of the sensor used. In order to accurately consider atmospheric influences, the atmosphere is modelled as a function of altitude regarding temperature, pressure and greenhouse gas concentrations. The atmospheric profiles are generated specifically for the time of the survey based on measurements, meteorological forecasts and generic models. The method was initially developed for application in urban contexts, as it is able to capture the pronounced three-dimensional character of such environments. However, due to the detailed consideration of elevation and atmospheric conditions, the method is also valuable for the analysis of rural areas. The included case studies covering two thermographic surveys of city area of Graz during daytime and nighttime demonstrate the capabilities and feasibility of the method. In relation to the detected brightness temperatures apparent to the sensor, the determined surface temperatures vary considerably and generally cover an increased temperature range. The two processed surface temperature maps of the city area of Graz are finally used to validate the method based on available temperature recordings.