Vanadium-based amorphous materials are an emerging category of lithium ion battery cathodes with high specific capacity and high voltage performance. In this study, we investigated the effect of fluorination on the performance of an amorphous vanadium-phosphorus-lithium (VPLi) cathode for lithium ion battery applications. Results show that the fluorinated product consists Li3VF6 and VF4 nanocrystals embedded in an amorphous phase when the V4+ content was in the range of 16.3% to 23.8%. VPFLi has an optimal specific capacity of 344.3 mAh g−1 in the first cycle and 269.7 mAh g−1 after 200 cycles at a current of 50 mA g−1 within the voltage range of 1.5–4.2 V. VPLi has an amorphous structure, and the reversible V4+/V5+ lithiation process corresponds to the conversion between V2O5 and Li2V2O5 during the charge–discharge cycle. Compared to VPLi, VF4 and Li3VF6 crystals were found to convert into LiVP2O7 in VPFLi, which led to the increased specific capacity. Simulation based on density functional theory show that fluorine for oxygen has led to the movement of Fermi level moves towards the edge of the conduction band. Charge mostly transferred from Li to O which contributed to the improved cathode stability. This study provides a new perspective towards selecting novel cathode for lithium-ion batteries.