The study presented herein concerns the mechanical properties of two common polymers for potential biomedical applications, PLA and PETG, processed through fused filament fabrication (FFF)—Material Extrusion (ME). For the uniaxial tension tests carried out, two printing orientations—XY (Horizontal, H) and YZ (Vertical, V)—were considered according to the general principles for part positioning, coordinates, and orientation typically used in additive manufacturing (AM). In addition, six specimens were tested for each printing orientation and material, providing insights into mechanical properties such as Tensile Strength, Young’s Modulus, and Ultimate Strain, suggesting the materials’ potential for biomedical applications. The experimental results were then compared with correspondent mechanical properties obtained from the literature for other polymers like ASA, PC, PP, ULTEM 9085, Copolyester, and Nylon. Thereafter, fatigue resistance curves (S-N curves) for PLA and PETG, printed along 45°, were determined at room temperature for a load ratio, R, of 0.2. Scanning electron microscope observations revealed fibre arrangements, compression/adhesion between layers, and fracture zones, shedding light on the failure mechanisms involved in the fatigue crack propagation of such materials and giving design reference values for future applications. In addition, fractographic analyses of the fatigue fracture surfaces were carried out, as well as X-ray Computed Tomography (XCT) and Thermogravimetric (TGA)/Differential Scanning Calorimetric (DSC) tests.