Long-term climate monitoring by universities provides fundamental data for various disciplines in the natural sciences. Kyoto University once managed ten university forest stations and is currently managing five. At these stations, climate data have been monitored almost since the establishment of each station until today, with the exception of the stations in foreign countries. We compiled and report the monthly climate data at these forest stations from the start of monitoring until December 2018. These data are important for investigating environmental changes in East Asia, including China (Taiwan), South Korea (Chosen), and Russia (Sakhalin, Karafuto) over the last 100 years. Long-term monitoring often involves minor and major changes in the monitoring procedures, devices, and even monitoring sites due to unavoidable circumstances, such as technological advances, changes in standard methods, and climatic and anthropogenic disasters. Therefore, associated metadata on the monitoring methods are also important. We also compiled metadata on changes in monitoring methods. In addition, to examine the effects of changes in the methods on the observed climate data, we compared the values recorded before and after the change for each climate variable at each monitoring site. Methodological changes affected only a few variables, with the exception of humidity. Careful interpretation may be required when a researcher uses humidity data in any analysis.