Deep-seated tumors are challenging pathologies to treat. Currently available approaches are limited, prompting innovative solutions. Hyperthermia treatment (HT) is a thermal oncological therapy that raises tumor temperature (40–44 °C for 60 min), enhancing radio- and chemotherapy. Biomaterials loaded with magnetic particles, called magnetic scaffolds (MagSs), are used as HT agents for cancer treatment using radiofrequency (RF) heating. MagSs can be manufactured via 3D printing using fused deposition modeling to create biomimetic architectures based on triply periodic minimal surfaces (TPMSs). TPMS-based MagSs have been tested in vitro for RF HT. However, there is a lack of understanding regarding the thermal properties of TPMS MagSs for RF hyperthermia. Significant discrepancies between simulated and measured temperatures have been reported, attributed to limited knowledge of the apparent thermal conductivity of MagSs. Since planning is crucial for HT, it is fundamental to determine the thermal properties of these heterogeneous and porous composite biomaterials. Magnetic polylactic acid (PLA) scaffolds, shaped in different TPMS geometries and variable porosities, were thermally investigated in this research study. A linear relationship was found between the apparent thermal conductivity of parallelepiped and cylindrical scaffolds, and the measured values were validated using a numerical model of the RF HT test.