The electrochemical performance as anodes in lithium-ion batteries (LIBs) of graphitized stacked-cup carbon nanofibers (CNFs) with different degree of structural order is investigated by galvanostatic cycling. To this end, two types of commercial CNFs (PR19 and PR24) bearing this microstructure were heat treated in the range of 1800-2800°C. The discharge capacity provided at the end of cycling, the capacity retention along cycling (cyclability) and the cycling efficiency (charge capacity/discharge capacity) of these nanomaterials improve significantly after heat treatment. Specifically, a progressive increase of the discharge capacity with the growth of the crystallites sizes (Lc, La) and the decrease of the structural defects (ID/It) is observed. All heat-treated CNFs exhibit cyclabilities > 80% after 50 cycles and efficiencies > 90%. Particularly outstanding is the performance of PR19-2800 which provides a discharge capacity of 295 mAh g−1 with capacity retention up to 88%. The CNFs heat treated at 2800°C also show good rate capabilities, keeping reversible capacities > 200 mAh g−1 at a 2C (744mA g−1) rate, and > 100 mAh g−1 after prolonged cycling (500 cycles) at a 1C rate, clearly outperforming synthetic graphite having micrometric particle size and much larger development of the crystalline structure.