The machining of hardened steels has always been a great challenge in metal cutting, particularly for drilling operations. Generally, drilling is the machining process that is most difficult to cool due to the tool’s geometry. The aim of this work is to determine the heat flux and the coefficient of convection in drilling using the inverse heat conduction method. Temperature was assessed during the drilling of hardened AISI H13 steel using the embedded thermocouple technique. Dry machining and two cooling/lubrication systems were used, and thermocouples were fixed at distances very close to the hole’s wall. Tests were replicated for each condition, and were carried out with new and worn drills. An analytical heat conduction model was used to calculate the temperature at tool–workpiece interface and to define the heat flux and the coefficient of convection. In all tests using new and worn out drills, the lowest temperatures and decrease of heat flux were observed using the flooded system, followed by the MQL, considering the dry condition as reference. The decrease of temperature was directly proportional to the amount of lubricant applied and was significant in the MQL system when compared to dry cutting.