In recent years, the Fused Deposition Modeling (FDM) method has been employed in the production of small-scale structural elements with moderate loads, such as small-unmanned aerial vehicles, sports equipment, dental implant molds, and similar applications. In these cases, the FDM technique can utilize polymers like Polyamide (PA), Polylactic Acid (PLA), and Acrylonitrile Butadiene Styrene (ABS) to manufacture structural components. Lightweight sandwich structures are utilized as structural elements in various industries due to their unique characteristics, high stiffness-to-weight ratio, and energy absorption capabilities. Although the number of studies on the mechanical properties of sandwich structures manufactured with FDM has increased in recent years, experimental data on the mechanical characteristics of sandwich structures manufactured with FDM under different thermal aging durations are still insufficient. Driven by this motivation, the energy absorption capabilities of sandwich structures with different four core geometries (i.e., circular, hexagonal, square, and triangular) were experimentally investigated under different thermal aging durations. The sandwich structures were manufactured from PLA material by the FDM method. Four different thermal aging durations, 0, 15, 30 and 45 days, were considered for environmental conditions. Quasi-static three-point bending experiments were conducted to assess the energy absorption capability of lightweight sandwich structures featuring diverse core topologies. The bending test results demonstrate that the core topology significantly affects the energy absorption abilities of sandwich structures. Moreover, fractographic analysis using scanning electron microscopy (SEM) was conducted to gain deeper insights into the impact of thermal aging on aged specimens. In addition, it was concluded that the energy absorption performances of all sandwich structures with different core structure topologies were adversely affected by increasing the thermal aging time.