Fused filament fabrication (FFF) 3D printing was used to fabricate continuous wire polymer composite (CWPC) heat flux sensors; the integrated wires acted as resistive sensing elements. Sensor configurations consisting of polylactic acid (PLA) with copper wire (Cu), PLA with nickel (Ni) wire, and thermoplastic polyurethane (TPU) with Cu wire were investigated. For each composition, samples with different numbers of layers were 3D printed to investigate the effect of sensor thickness on performance. Element spacing, polymer conductivity, and wire temperature coefficient of resistances were quantified. Performance testing of the 3D-printed CWPC as a heat flux sensor showed promising results for all compositions and demonstrated their ability to be used as heat flux sensors for low temperature and low heat flux applications. Measurement errors were less than 17% for all configurations and less than 10% for 2-layer samples at the higher heat fluxes. A case study demonstrated the use of a 3D-printed flexible CWPC heat flux sensor to estimate heat loss from an insulated system with good accuracy. This sensor fabrication approach can potentially be employed in a wide range of applications because it allows for custom geometries and can use different types of polymers and sensing elements.