The friction element welding (FEW) process is a thermo-mechanical approach toward joining of dissimilar materials using an auxiliary consumable element which is welded to a base material which is harder than its counterpart. It is necessary to understand the transient thermal response generated during the various stages of FEW process to gain insight into the influence of FEW process parameters on the physics of the FEW process along with microstructural changes of the weld zone interface. However, due to the challenges associated with accessibility of the welding interface during the FEW process, the experimental investigation of thermal behavior is rendered to be highly complicated. In this work, an array of micro thin film thermocouples (TFTCs) were fabricated on JSC980 steel substrates, which were used to measure the transient temperatures generated at the vicinity of the friction element during the FEW joining of Al6005 and JSC980 sheets. The high spatial and temporal resolution of the TFTCs enabled us to observe the overall transient temperature response generated during the four stages of the FEW process – penetration, cleaning, welding and compression. Analysis of the applied compressive forces on the friction element and the resulting torque generated due to the increased frictional resistance of the element tip against the JSC980 surface showed that peak process temperatures are reached during the cleaning and welding steps of the FEW process. The experimental temperature measurements obtained in this work could be utilized to validate and improve analytical and numerical models of the temperature evolution FEW process. This work also lays the necessary groundwork for further investigation into the microstructural characteristics of the weld zone dependent on the temperatures reached at each step of the FEW process.