While first order perturbation theory is routinely used in quantum Monte Carlo (QMC) calculations, higher-order terms present significant numerical challenges. We present a new approach for computing perturbative corrections in projection QMC calculations. We demonstrate the method by computing nuclear ground state energies up to second order for a realistic chiral interaction. We calculate the binding energies of several light nuclei up to ^{16}O by expanding the Hamiltonian around the Wigner SU(4) limit and find good agreement with data. In contrast to the natural ordering of the perturbative series, we find remarkably large second-order energy corrections. This occurs because the perturbing interactions break the symmetries of the unperturbed Hamiltonian. Our method is free from the sign problem and can be applied to QMC calculations for many-body systems in nuclear physics, condensed matter physics, ultracold atoms, and quantum chemistry.