The Schwinger effect in the presence of instantons is considered in this paper. Using AdS/CFT correspondence in the near horizon limit of the D3+D($-1$)-brane background, we calculate the total potential of a quark-antiquark pair in an external electric field. It is shown that instantons tend to suppress the pair creation effect and increase the critical electric field above which the pairs are produced freely without any suppression. Interestingly, no other critical electric field, common for all confining field theories, is observed here at finite temperature. However, as expected we find such a critical electric field at zero temperature. The pair production rate evaluated by the calculation of the expectation value of the circular Wilson loop also confirms this result.