The thermal conductance of a single silicon nanojunction was measured based on a Lab-in-a-TEM (microelectromechanical systems in a transmission electron microscope) technique and was found to be at least 2 orders of magnitude larger than the ones of long nanowires in the 380–460 K temperature range. The predominance of ballistic phonon transport appears as the best hypothesis to retrieve quantitative predictions despite the geometrical irregularity of the junction. The measurement is based on a MEMS structure including an electrostatic actuator that allows producing nanojunctions with the accuracy based on the resolution of a transmission electron microscope. The thermal conductance is measured by two integrated resistors that are simultaneously heating and measuring the local temperatures at the nearest of the nanojunction. The considerable thermal conductance of short nanojunctions constitutes a new key element in the design of nanosystems and in the understanding of the damaging of mechanical micronanocontacts. This conducting behavior is also paving the way for the development of nanoscale cooling devices as well as of the recent phononic information technology.