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Parity-time (PT) symmetric non-Hermitian Hamiltonians bring about many novel features and interesting applications such as quantum gates faster than those in Hermitian systems, and topological state transfer. The performance of evolutions under $\mathcal{PT}$-symmetric Hamiltonians is degraded by the inevitable noise and errors due to system-environment interaction and experimental imperfections. In contrast to Hermitian Hamiltonians, the fluctuations in dissipative beams that are utilized to generate non-Hermitian contributions in the PT-symmetric Hamiltonians cause additional errors. Here we achieve the protection of PT-symmetric Hamiltonians against noise acting along the qubit's quantization axis by combining quantum evolutions with dynamical decoupling sequences. We demonstrate the performance of our method by numerical simulations. Realistic noise sources and parameters are chosen including: constant detuning error, time-varying detuning noise and dissipative-beam noise. The fidelities of the protected evolutions are well above the unprotected ones under all the above situations. Our work paves the way for further studies and applications of non-Hermitian $\mathcal{PT}$-symmetric physics in noisy quantum systems.