In this experimental work, 3D printed honeycomb structures were fabricated using carbon fiber (CF) with three different matrices: Polylactic acid (PLA), Acrylonitrile Butadiene Styrene (ABS), and Polyethylene terephthalate glycol (PETG). All the fabricated composite samples were subjected to compressive strength testing, and their values were analysed by varying cell size and wall thickness of each composite sample. The face plates were fabricated using vacuum assisted resin transfer moulding technique. For the honeycomb designs, equivalent surface areas were chosen with variations in cell width (6–12 mm) and wall thickness (0.8–1.6 mm). However, the cell height of the samples remained constant at 42 mm. Results revealed that the composites made with CF/PLA using a 12 mm cell width, 1.6 mm wall thickness, and 42 mm cell height exhibited improved compressive strength (2122 MPa). Furthermore, these experimental responses were quantitatively investigated through LSDYNA software. The finite element analysis reported an accuracy ranging from 70 to 90% comparing to the experimental findings.