Provided is a method of manufacturing a lithium ion secondary battery. The method includes a step of initially charging the battery. The step includes: a first step of charging the battery such that a voltage Vt of the battery is increased to a first voltage Vh which is in a lower decomposition range Ad; a second step of holding the voltage Vt of the battery at the first voltage Vh; and a third step of charging the battery to a second voltage Ve, which is higher than the first voltage Vh, after the second step.