The σ-1 receptor (Sig1R) is widely expressed in the CNS, where it has a neuroprotective role in ischemia and stroke and an involvement in schizophrenia. The Sig1R interacts functionally with a variety of ion channels, including the NMDA receptor (NMDAR). Here, we used atomic force microscopy (AFM) imaging to investigate the interaction between the Sig1R and the NMDAR. The Sig1R bound directly to GluN1/GluN2A NMDAR heterotetramers. Furthermore, the mean angle between pairs of bound Sig1Rs was 72°. This result suggested that the Sig1R interacts with either GluN1 or GluN2A, but not both, and supports our recent demonstration that the NMDAR subunits adopt an adjacent (i.e., 1/1/2/2) arrangement. The Sig1R could be coisolated with GluN1 but not with GluN2A, indicating that GluN1 is its specific target within the NMDAR. Consistent with this conclusion, AFM imaging of coisolated Sig1R and GluN1 revealed GluN1 dimers decorated with Sig1Rs. In situ proximity ligation assays demonstrated that the Sig1R interacts with GluN1 (but not with GluN2A) within intact cells and also that its C terminus is extracellular. We conclude that the Sig1R binds to the GluN1/GluN2A NMDAR specifically via the GluN1 subunit. This interaction likely accounts for at least some of the modulatory effects of Sig1R ligands on the NMDAR.