Results of paleoclimatic analysis of geothermal data in the Middle and Southern Urals for different time intervals are presented. Climate reconstruction for the past millennium was made using data from 44 boreholes, and the magnitude of the Wurm–Holocene warming event was estimated based on data from two deep boreholes. The method of functional space inversion was used. The resolution of the method for reconstruction of various climatic events in the past was investigated. Parameters specified a priori and the required duration of the period to be reconstructed were chosen from the results of numerical modeling. According to the inversion results, the ground surface temperature at the maximum of the Medieval Warm Period in 1100–1200 was approximately the same as the present temperature, and at the minimum of the Little Ice Age around 1720, it was 1.2–3 °C lower than at present. The subsequent temperature rise was more pronounced in the past century. The magnitude of the Wurm–Holocene warming event, reconstructed using data from two deep boreholes is 10–11 °C.