Samples of composite materials based on high-performance semicrystalline polyimide R-BAPB (based on the dianhydride R: 1,3-bis-(3′,4,-dicarboxyphenoxy)benzene and diamine BAPB: 4,4′-bis-(4″-aminophenoxy)diphenyl)) filled with carbon nanofibers and micron-sized discrete carbon fibers were obtained by FFF printing for the first time. The viscosity of melts of the composites based on R-BAPB, thermal, mechanical characteristics of the obtained composite samples, their internal structure, and biocompatibility were studied. Simultaneously with FFF printing, samples were obtained by injection molding. The optimal concentrations of carbon fillers in polyimide R-BAPB for their further use in FFF printing were determined. The effect of the incorporation of carbon fillers on the porosity of the printed samples was investigated. It was shown that the incorporation of carbon nanofibers reduces the porosity of the printed samples, which leads to an increase in deformation at break. Modification of polyimide with discrete carbon fibers increases the strength and Young’s modulus sufficiently but decreases the deformation at break. The cytotoxicity analysis showed that the obtained composite materials are bioinert.