The objectives of this work are to determine an accurate temperature feedback strategy and to develop a closed-loop feedback control system for temperature in friction stir welding (FSW). FSW is a novel joining technology enabling welds with excellent metallurgical and mechanical properties, as well as significant energy consumption and cost savings. However, numerous parameter and condition variations are present in the FSW production environment that can adversely affect weld quality, which has made extensive automation of this process impossible to date. To enable large scale automation while maintaining weld quality, techniques to control the FSW process in the presence of unknown disturbances must be developed. One process variable that must be controlled to maintain uniform weld quality under the inherent workpiece variability (thermal constraints, material properties, geometry, etc.) is the weld zone temperature. Our hypothesis is that the weld zone temperature can be controlled, which can help in controlling the weld quality. A wireless data acquisition system was built to measure temperatures at the tool-workpiece interface. A thermocouple was placed in a through hole right at the interface of tool and workpiece so that the tip is in contact with the workpiece material. This measurement strategy reveals temperature variations within a single rotation of the tool in real time. In order to automate the system, a first order process model with transport delay was experimentally developed that captures the physics between spindle speed and measured interface temperature. The model has a time constant of 110 ms and a delay time of 85 ms. Using this temperature measurement technique, a closed-loop temperature control system with a bandwidth of 0.3 Hz was developed. Interface temperatures in the range from 555 °C to 575 °C were commanded to an integral controller, which regulated the spindle speed between 850 rpm and 1250 rpm to adjust the heat generation and achieve the desired interface temperatures in 6061-T6 aluminum. To simulate changes in thermal boundary conditions, backing plates of different thermal diffusivities were found to effectively alter the heat flow, hence, weld zone temperature. The integral controller that manipulates spindle speed is applied when welding during these intentionally introduced weld disturbances. The measured temperature stayed within ±5 °C after introducing the disturbance, compared to a 50 °C change in temperature when no control was applied.