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Motivated by the recent advances in modelling the pseudo-Hermitian Hamiltonian (pHH) systems using superconducting qubits we analyze their quantum dynamics subject to a small time-dependent perturbation. In particular, We develop the linear response theory formulation suitable for application to various pHH systems and compare it to the ones available in the literature. We derive analytical expressions for the generalized temporal quantum-mechanical correlation function $C(t)$ and the time-dependent dynamic susceptibility $χ(t) \propto \text{Im} ~C(t)$. We apply our results to two \textit{PT}-symmetric non-Hermitian quantum systems: a single qubit and two unbiased/biased qubits coupled by the exchange interaction. For both systems we obtain the eigenvalues and eigenfunctions of the Hamiltonian, identify \textit{PT}-symmetry unbroken and broken quantum phases and quantum phase transitions between them. The temporal oscillations of the dynamic susceptibility of the qubits polarization ($z$-projection of the total spin), $χ(t)$, relate to {\it ac} induced transitions between different eigenstates and we analyze the dependencies of the oscillations frequency and the amplitude on the gain/loss parameter $γ$ and the interaction strength $g$. Studying the time dependence of $χ(t)$ we observe different types of oscillations, i.e. undamped, heavily damped and amplified ones, related to the transitions between eigenstates with broken (unbroken) $PT$-symmetry. These predictions can be verified in the microwave transmission experiments allowing controlled simulation of the pHH systems.