Two classes of preceramic polymers, namely polysilazane and polysilylcarbodiimide, with branched and linear molecular structure were pyrolyzed at 1100 °C under argon atmosphere. The resulting nanostructured polymer-derived SiCN ceramics were characterized by means of elemental analysis, X-ray diffraction, scanning electron microscopy and Raman spectroscopy. All investigated ceramics are amorphous and contain a disordered free carbon phase of 2–2.5 nm in size. Electrochemical characterization reveals that the polysilazane-derived electrodes demonstrate higher capacity and stability during subsequent lithium insertion/extraction with different currents than those of the polysilylcarbodiimide-based electrodes. The highest lithium extraction capacity of 724 mA h g−1 is recovered for the sample derived from branched polysilazane whereas the best polysilylcarbodiimide-derived sample recovers 612 mA h g−1. Moreover, the polysilazane-derived samples deliver a higher fraction of capacity recovered below 1.5 V. The electrochemical performance is found to be dependent on the molecular structure (silazane vs. silylcarbodiimide) of the preceramic polymer, while there is no effect associated with the amount of branching (silsesquiazane vs. silazane and silsesquicarbodiimide vs. silylcarbodiimide). The influence of “micropore activity” and oxygen content on the electrochemical performance of polymer-derived silicon carbonitrides is addressed.