Quantum measurements are crucial for extracting information from quantum systems, but they are error-prone due to hardware imperfections in near-term devices. Measurement errors can be mitigated through classical post-processing, based on the assumption of a classical noise model. However, the coherence of quantum measurements leads to unavoidable quantum noise that defies this assumption. In this work, we introduce a two-stage procedure to systematically tackle such quantum noise in measurements. The idea is intuitive: we first detect and then eliminate quantum noise. In the first stage, inspired by coherence witness in the resource theory of quantum coherence, we design an efficient method to detect quantum noise. It works by fitting the difference between two measurement statistics to the Fourier series, where the statistics are obtained using maximally coherent states with relative phase and maximally mixed states as inputs. The fitting coefficients quantitatively benchmark quantum noise. In the second stage, we design various methods to eliminate quantum noise, inspired by the Pauli twirling technique. They work by executing randomly sampled Pauli gates before the measurement device and conditionally flipping the measurement outcomes in such a way that the effective measurement device contains only classical noise. We numerically demonstrate the two-stage procedure’s feasibility on the Baidu Quantum Platform. Notably, the results reveal significant suppression of quantum noise in measurement devices and substantial enhancement in quantum computation accuracy. We highlight that the two-stage procedure complements existing measurement error mitigation techniques, and they together form a standard toolbox for manipulating measurement errors in near-term quantum devices.