We compute the electric dipole moment (EDM) of the deuteron in the holographic QCD model of Witten-Sakai-Sugimoto. Previously, the leading contribution to the EDM of nucleons was computed, finding opposite values for the proton and the neutron which then cancel each other in the deuteron state. Here we compute the next-to-leading order contribution which provides a splitting between their absolute value. At large $N_{rm c}$ and large t Hooft coupling $lambda$, nuclei are bound states of almost isolated nucleons. In particular, we find that in this limit the deuteron EDM is given by the splitting between proton and neutron EDMs. Our estimate for the deuteron EDM extrapolated to the physical values of $N_{rm c}$, $lambda$, $M_{rm KK}$ and $m_q$ is $mathcal{D}_D = -0.92times 10^{-16} theta e cdot {cm}$. This is consistent, in sign and magnitude, with results found previously in the literature and obtained using completely different methods.
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