Common rail (CR) diesel fuel injection systems are very sensitive to variations in fuel properties, thus the impact of alternative fuels on the durability of the injection system should be investigated when considering the use of alternative fuels. This work studies a high-pressure CR (HPCR) diesel fuel injection system operating for 400 h in an injection test bench, using a fuel blend composed of an alternative paraffinic fuel and conventional diesel (50PF50D). The alternative fuel does not have aromatic components and has lower density than conventional diesel fuel. The injection system durability study was carried out under typical injection pressure and fuel temperature for the fuel pump, the common rail and the injector. The results show that the HPCR fuel injection system and its components (e.g., piston, spring, cylinder, driveshaft and cam) have no indication of damage, wear or change in surface roughness. The absence of internal wear to the components of the injection system is supported by the approximately constant total flow rate that reaches the injector during the whole the 400 h of the experiment. However, the size of the injector nozzle holes was decreased (approximately 12%), being consistent with the increase in the return fuel flow of the injector and rail (approximately 13%) after the completion of the study. Overall, the injection system maintained its operability during the whole duration of the durability study, which encourages the use of paraffinic fuels as an alternative to conventional diesel fuel.