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Junction temperature of high power light emitting diodes (LEDs), which is crucial for the thermal management of solid-state lighting, needs to be measured accurately. In this paper, a dynamic junction temperature measurement system for LEDs was proposed and the calibration including instrument calibration and factor K calibration were presented. The influence of the fast switch time in dynamic junction temperature test was analyzed and measurement errors caused by sampling delay were quantified. To prove the accuracy of the present system, comparison experiment was conducted. It shows a good agreement between the experimental data and reference value. Experiments also show that the measurement accuracy of the instrument can be up to 0.1 °C, and the standard error of temperature measurement can be controlled within 1%.