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Numerical difficulties associated with computing matrix elements of operators between Hartree–Fock–Bogoliubov (HFB) wavefunctions have plagued the development of HFB-based many-body theories for decades. The problem arises from divisions by zero in the standard formulation of the nonorthogonal Wick’s theorem in the limit of vanishing HFB overlap. In this Communication, we present a robust formulation of Wick’s theorem that stays well-behaved regardless of whether the HFB states are orthogonal or not. This new formulation ensures cancellation between the zeros of the overlap and the poles of the Pfaffian, which appears naturally in fermionic systems. Our formula explicitly eliminates self-interaction, which otherwise causes additional numerical challenges. A computationally efficient version of our formalism enables robust symmetry-projected HFB calculations with the same computational cost as mean-field theories. Moreover, we avoid potentially diverging normalization factors by introducing a robust normalization procedure. The resulting formalism treats even and odd number of particles on equal footing and reduces to Hartree–Fock as a natural limit. As proof of concept, we present a numerically stable and accurate solution to a Jordan–Wigner-transformed Hamiltonian, whose singularities motivated the present work. Our robust formulation of Wick’s theorem is a most promising development for methods using quasiparticle vacuum states.