Accurate heat flux measurements are needed to gain a better knowledge of the thermal performance of buildings and to evaluate the heat exchange among various parts of a building envelope. Heat flux meters (HFMs) are commonly used both in laboratory applications and in situ for measuring one-dimensional heat fluxes and, thus, estimating the thermal transmittance of material samples and existing buildings components. Building applications often requires heat flux measurements below 100 W · m−2. However, a standard reference system generating such a low heat flux is available only in a few national metrology institutes (NMIs). In this work, a numerical study aimed at designing an HFM calibration apparatus operating in the heat flux range from 5 W·m−2 to 100 W · m−2 is presented. Predictions about the metrological performance of such a calibration system were estimated by numerical modeling exploiting a commercial FEM code (COMSOL®). On the basis of the modeling results, an engineered design of such an apparatus was developed and discussed in detail. The system was designed for two different purposes: (i) for measuring the thermal conductivity of insulators and (ii) for calibrating an HFM with an absolute method (i.e., by measuring the applied power from the heater and its active cross section) or by a relative method (i.e., by measuring the temperature drop across a reference material of known thickness and thermal conductivity). The numerical investigations show that in order to minimize the uncertainty of the generated heat flux, a fine temperature control on the thermal guard is needed. The predicted standard uncertainty is within 2% at 10W·m−2 and within 0.5% at 100 W · m−2.