There is provided a lithium ion secondary battery exhibiting a high capacity retention rate over a long period. There is also provided a method for manufacturing a lithium ion secondary battery including a positive electrode, a negative electrode containing a negative electrode active material layer containing a graphite, an aprotic electrolyte solution containing a sulfonate ester having at least two sulfonyl groups, and a packaging material including a laminate film involving the positive electrode, the negative electrode and the aprotic electrolyte solution, the method including: enclosing the positive electrode, the negative electrode and the aprotic electrolyte solution in the packaging material to fabricate a lithium ion secondary battery before pre-charge; pre-charging the lithium ion secondary battery; and opening the enclosure of the packaging material of the lithium ion secondary battery after pre-charge, thereafter vacuum sealing the packaging material, and regularly charging the lithium ion secondary battery after pre-charge, wherein the current for the pre-charge is 0.05 to 0.25 C, and the voltage thereof is 3.3 to 3.5 V.