The objective of this work is to develop an improved temperature measurement system for friction stir welding (FSW). FSW is a solid-state joining process enabling welds with excellent metallurgical and mechanical properties, as well as significant energy consumption and cost savings compared to traditional fusion welding processes. The measurement of temperatures during FSW is needed for process monitoring, heat transfer model verification and process control, but current methods have limitations due to their restricted spatial and temporal resolution. Previous work showed that temperatures at the tool shoulder-workpiece interface can be measured and utilized for closed-loop control of temperature. Adding an additional thermocouple at the tool pin-workpiece interface and performing a calibration of the measurement to gain better insight into the temperature distribution in the weld zone improved the method. Both thermocouples were placed in through holes right at the interface of tool so that the sheaths are in direct contact with the workpiece material. This measurement strategy reveals dynamic temperature variations at the shoulder and the pin within a single rotation of the tool in real-time. It was found that the highest temperatures are at the shoulder interface between the advancing side and the trailing edge of the tool, closer to the advancing side. The temperature distribution was mostly affected by travel speed and the temperature difference within one tool rotation was found to be between 10 °C and 50 °C, depending on the process parameters. The dynamic temperature measurements obtained with the current system are of unmatched resolution, fast, and reliable and are likely to be of interest for both fundamental studies and process control of FSW.