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We investigate the non-perturbative effects of a deformation of the Mathieu differential equation consistent with $\mathcal{PT}$ symmetry. First, we develop a connection between the non-Hermitian and Hermitian scenarios by a reparameterization in the complex plane, followed by a restriction of the $\mathcal{PT}$ deformation parameter. The latter is responsible for preserving the information about $\mathcal{PT}$ symmetry when we choose to work in the Hermitian scenario. We note that this factor is present in all non-perturbative results and in the transseries representation of the deformed Mathieu partition function that we have obtained. In quantum mechanics, we found that the deformation parameter of $\mathcal{PT}$ symmetry has an effect on the real instanton solution for the deformed Mathieu potential in the Hermitian scenario. As its value increases, the non-Hermiticity factor makes it smoother for the instanton to pass from one minimum to another, that is, it modifies the instanton width. The explanation for this lies in the fact that the height of the potential barrier decreases as we increase the value of the deformation parameter. We present how this effect extends to the multi-instanton level and to the bounce limit of an instanton-anti-instanton pair. As an application of the obtained results, we show that the equation of motion under a tilted version of the potential in the Hermitian scenario compares to the resistively shunted junction (RSJ) model for the Josephson junction.