Honeycomb sandwich structures are widely used in lightweight applications. Usually, these structures are subjected to extreme loading conditions, leading to potential failures due to delamination and debonding between the face sheet and the honeycomb core. Therefore, the present study is focused on the mechanical characterisation of honeycomb sandwich structures fabricated using advanced 3D printing technology. The continuous carbon fibres and ONYX-FR matrix materials have been used as raw materials for 3D printing of the specimens needed for various mechanical characterization testing; ONYX-FR is a commercial trade name for flame retardant short carbon fibre filled nylon filaments, used as a reinforcing material in Morkforged 3D printer. Edgewise and flatwise compression tests have been conducted for different configurations of honeycomb sandwich structures, fabricated by varying the face sheet thickness and core cell size, while keeping the core cell thickness and core height constant. Based on these tests, the proposed structure with face sheet thickness of 3.2 mm and a core cell size of 12.7 mm exhibited the highest energy absorption and prevented delamination and debonding failures. Therefore, 3D printing technology can also be considered as an alternative method for sandwich structure fabrication. However, detailed parametric studies still need to be conducted to meet various other structural integrity criteria related to the lightweight applications.