We report a photoluminescence imaging system for locating single quantum emitters with respect to alignment features. Samples are interrogated in a 4 K closed-cycle cryostat by a high numerical aperture (NA = 0.9, 100× magnification) objective that sits within the cryostat, enabling high efficiency collection of emitted photons without image distortions due to the cryostat windows. The locations of single InAs/GaAs quantum dots within a >50 μm × 50 μm field of view are determined with ≈4.5 nm uncertainty (one standard deviation) in a 1 s long acquisition. The uncertainty is determined through a combination of a maximum likelihood estimate for localizing the quantum dot emission, and a cross correlation method for determining the alignment mark center. This location technique can be an important step in the high-throughput creation of nanophotonic devices that rely upon the interaction of highly confined optical modes with single quantum emitters.