Using the AdS/CFT correspondence, we calculate the vacuum decay rate for the Schwinger effect in confining large N (c) gauge theories. The instability is induced by thecorrespondence, we calculate the vacuum quark antiquark pair creation triggered by strong electromagnetic fields. The decay rate is obtained as the imaginary part of the Euler-Heisenberg effective Lagrangian evaluated from the D-brane action with a constant electromagnetic field in holographic QCD models such as the Sakai-Sugimoto model and the deformed Sakai-Sugimoto model. The decay rate is found to increase with the magnetic field parallel to the electric field, while it decreases with the magnetic field perpendicular to the electric field. We discuss generic features of a critical electric field as a function of the magnetic field and the QCD string tension in the Sakai-Sugimoto model.