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Motivated by recent development of the concept of the disorder operator and its relation with entanglement entropy in bosonic systems, here we show the disorder operator successfully probes many aspects of quantum entanglement in fermionic many-body systems. From both analytical and numerical computations in free and interacting fermion systems in 1D and 2D, we find the disorder operator and the entanglement entropy exhibit similar universal scaling behavior, as a function of the boundary length of the subsystem, but with subtle yet important differences. In 1D they both follow the $\log{L}$ scaling behavior with the coefficient determined by the Luttinger parameter for disorder operator, and the conformal central charge for entanglement entropy. In 2D they both show the universal $L\log L$ scaling behavior in free and interacting Fermi liquid states, with the coefficients depending on the geometry of the Fermi surfaces. However at a 2D quantum critical point with non-Fermi-liquid state, extra symmetry information is needed in the design of the disorder operator, so as to reveal the critical fluctuations as does the entanglement entropy. Our results demonstrate the fermion disorder operator can be used to probe quantum many-body entanglement related to global symmetry, and provides new tools to explore the still largely unknown territory of highly entangled fermion quantum matter in 2 or higher dimensions.