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Abstract Inspired by significant local distortions found near vacancies in a neutron pair distribution function analysis study (G. King et al.,Inorg. Chem.2012, 51, 13060) of Sr₂MSbO_5.5(M = Ca and Sr), this computational study finds minimum‐energy structures with these and related distortions using density functional theory (DFT) with the Perdew‐Burke‐Ernzerhof (PBE) functional as implemented in the Vienna Ab Initio Simulations Package (VASP) (G. Kresse and J. Furthmüller,Phys. Rev. B, 1996, 54, 11169; G. Kresse and J. Hafner,Phys. Rev. B, 1993, 47, 558; G. Kresse and J. Furthmüller,Comput. Mater. Sci., 1996, 6, 15). All structures were optimized using the conjugate gradient method. The global minima found for both systems featured trigonal bipyramid SbO₅structures and edge sharing with M‐centered polyhedra. However, while calcium ions occupied full and partial octahedra, the larger strontium ions were more commonly found in full and partial pentagonal bipyramids. Molecular dynamics with velocity rescaling at1200K revealed movements of the oxygen vacancy via polyhedral rotations. This work highlights the need to consider both square pyramid to trigonal bipyramid rearrangements around small ions and rotational polyhedral movements in simulating oxygen vacancy conduction in oxygen‐deficient double perovskites.