The negatively charged nitrogen vacancy (NV−) center in a diamond is a nanometer-sized defect with very sensitive properties that can be manipulated, for example, for single-molecule photoluminescence and nuclear magnetic resonance sensing, as a single photon source for quantum cryptography and as a qubit in room temperature quantum computing. To have a minimal perturbation of its properties, it is important to isolate the NV-center from other defects. One type of the extended defects that can be common in diamonds is the intrinsic stacking fault (ISF) associated with dislocations. In this work, we use density functional theory simulations to investigate how the distance between the NV− center and an ISF affects its properties, including the transition energies, spin density, and energy eigenvalues in the Kohn–Sham bandgap. We have found that the NV-center properties are only slightly perturbed when placed in the vicinity of an ISF. Even for an interdistance of only 3.8 Å between the NV-center and the ISF, the decrease in its zero phonon line (ZPL) energy is less than 6.8%. To more significantly perturb the ZPL, the NV-center has to be placed inside the stacking fault glide plane (11.3% decrease). The changes in ZPL are in the majority of cases lower than the bulk value, which can be used to guide experimental observations. We find that the NV-center is only weakly interacting with ISFs, which in addition to a small bulk conversion depth of 5 Å to a diamond surface is important for their technological use.