Microfluidic devices made from polydimethylsiloxane (PDMS) have diverse biomedical applications. However, due to the poor printability of PDMS, current 3D printing techniques are rarely used to fabricate microfluidic devices. This study aims to investigate a fumed silica-PDMS suspension that can function as a matrix bath for embedded 3D printing (e-3DP) purposes, making it technically feasible to print microfluidic chips with complex embedded channels via low-cost extrusion 3D printing. The rheological properties, mechanical properties, transparency, and filament fidelity of the fumed silica-PDMS suspension have been systematically studied. It is found that the addition of fumed silica particles can effectively change PDMS from a viscous solution to a yield-stress suspension with suitable rheological properties for e-3DP. Also, the mechanical properties of the crosslinked fumed silica-PDMS are enhanced with an increased concentration of fumed silica. Although the transparency of PDMS has been lessened by mixing it with fumed silica particles, the visibility of the printed microfluidic chips is still acceptable. The filament fidelity has been studied by embedded printing filaments using a sacrificial ink in the fumed silica-PDMS suspension. Finally, two representative microfluidic chips for biomedical applications have been successfully printed to validate the effectiveness of the proposed fumed silica-PDMS suspension-enabled e-3DP method.