We demonstrate a prototype through-wafer microfluidic structure in bulk silicon carbide (SiC) fabricated by femtosecond laser micromachining. The effects of laser fluence and scanning speed on the laser-affected zone are also investigated. Furthermore, the wettability of the laser-affected surface for the target liquid, mineral oil, is examined. Microchannels of various cross-sectional shapes are fabricated by the femtosecond laser and their effects on the liquid flow are simulated and compared. This fabrication approach offers a fast and efficient route to implement SiC-based through-wafer micro-structures, which are not able to be realized using other methods such as chemical etching. The flexibility of manufacturing 3D structures based on this fabrication method enables more complex structures as well. Smooth liquid flow in the microchannels of the bulk SiC substrate is presented. The work shown here paves a new way for various applications such as reliable microfluidic systems in a high-temperature, high radioactivity, and corrosive environment, and could be combined with SiC wafer-to-wafer bonding to realize a plethora of novel microelectromechanical (MEMS) structures.