Provided are an electrical deionization apparatus which can improve boron removal performance and the efficiency of removing ionic components, and a system and method for manufacturing ultrapure water using same. The electrical deionization apparatus has: an electrical deionization stack; a positive electrode and a negative electrode for applying voltage to the electrical deionization stack; and a power supply device for applying DC voltage between the positive electrode and the negative electrode, wherein the electrical deionization stack has: positive electrode chambers having positive electrodes; negative electrode chambers having negative electrodes; a plurality of anion exchange membranes and cation exchange membranes alternately arranged between the positive electrode chambers and the negative electrode chambers; concentration chambers and desalination chambers alternately arranged between the plurality of anion exchange membranes and cation exchange membranes; and ion exchangers filled into the desalination chambers. The DC voltage supplied by the power supply device satisfies the following equation, where Vmax represents the maximum voltage and Vmin represents the minimum voltage during a predetermined period of time. Equation: (Vmax-Vmin)/(Vmax+Vmin) ≤ 0.3.