Permafrost lies close to the surface of the day, therefore, it is able to quickly respond to modern climatic changes. Under these conditions, the goal of understanding the evolution of permafrost in the near future requires monitoring studies of the current state of permafrost and, first of all, its thermal conditions. In this work, based on the experience of many years of research at the Melnikov Permafrost Institute of Siberian Branch of the Russian Academy of Science (MPI SB RAS), methodological and technical issues of equipping experimental sites for monitoring the thermal state of permafrost in Eastern Siberia are considered. It is demonstrated that the reliability of permafrost thermal monitoring depends not only on measurement devices used but also on proper borehole system design and adequate choice of a method for active-layer thickness measurement depending on soil composition and properties. The use of protective tubes significantly lengthens the life of sensors in soils. A method of protecting the loggers from surface waters is recommended.