An apparatus of manufacturing an elastomeric cell frame for a fuel cell may include, as the apparatus of manufacturing the elastomeric cell frame including an insert in which a membrane electrode assembly and a gas diffusion layer have been bonded, and a sheet-like elastomeric frame made of a thermoplastic elastomer (TPE) integrated into an external area of the insert to form the unit cell of the fuel cell, a lower jig module accommodated so that the overlapping area, in which the insert and the elastomeric frame overlap at a predetermined area, is accommodated, and an upper jig module mounted above the lower jig module to provide heat and pressure to the overlapping area to thermally bond an interface between the insert and the elastomeric frame in the overlapping area.