One of the biggest challenges of fused deposition modeling (FDM)/fused filament fabrication (FFF) 3D-printing is maintaining consistent quality of layer-to-layer adhesion, and on the larger scale, homogeneity of material inside the whole printed object. An approach for mitigating and/or resolving those problems, based on the rapid and reliable control of the extruded material temperature during the printing process, was proposed. High frequency induction heating of the nozzle with a minimum mass (<1 g) was used. To ensure the required dynamic characteristics of heating and cooling processes in a high power (peak power > 300 W) heating system, an indirect (eddy current) temperature measurement method was proposed. It is based on dynamic analysis over various temperature-dependent parameters directly in the process of heating. To ensure better temperature measurement accuracy, a series-parallel resonant circuit containing an induction heating coil, an approach of desired signal detection, algorithms for digital signal processing and a regression model that determines the dependence of the desired signal on temperature and magnetic field strength were proposed. The testbed system designed to confirm the results of the conducted research showed the effectiveness of the proposed indirect measurement method. With an accuracy of ±3 °C, the measurement time is 20 ms in the operating temperature range from 50 to 350 °C. The designed temperature control system based on an indirect measurement method will provide high mechanical properties and consistent quality of printed objects.