We present a two-flavor QCD calculation of B K on a 16 3 × 32 lattice at a ∼ 0.12 fm (or equivalently a −1 =1.67 GeV). Both valence and sea quarks are described by the overlap fermion formulation. The matching factor is calculated nonperturbatively with the so-called RI/MOM scheme. We find that the lattice data are well described by the next-to-leading order (NLO) partially quenched chiral perturbation theory (PQChPT) up to around a half of the strange quark mass (m phys s /2). The data at quark masses heavier than m phys s /2 are fitted including a part of next-to-next-to-leading order terms. We obtain B MS K (2 GeV) = 0.537(4)(40), where the first error is statistical and the second is an estimate of systematic uncertainties from finite volume, fixing topology, the matching factor, and the scale setting.