Disclosed herein is an apparatus for manufacturing a secondary battery by performing insert injection molding with respect to a portion of a battery cell while the battery cell is located in a mold, wherein the apparatus comprises a pair of upper and lower molds, at which are formed shapes corresponding to the battery cell, the upper and lower molds are provided at the inside surfaces thereof with elastic members, and the elastic members are constructed in a structure in which the elastic members support a cell body of the battery cell and isolate a non-molding region from a molding region while the battery cell is mounted in the upper and lower molds. The secondary battery manufacturing apparatus according to the present invention has the effect of preventing a battery case from being damaged due to the contact between the battery case and the mold when the mold is brought into tight contact with the cell body of the battery cell during insert injection molding to form a molding member at a specific region of the secondary battery, and effectively preventing a material for insert injection molding, which is injected into the molding region, from being injected into the non-molding region.