Cell transplantation is a promising strategy for treating degenerative eye disorders for which no curative therapies exist, including age-related macular degeneration (AMD), diabetic retinopathy, and glaucoma. While past and ongoing clinical trials of ocular cell transplantation have demonstrated encouraging findings, our insight into their successes and failures is limited, in large part due to the difficulty of following the fate of the transplanted cells in the human eye. Here we explore the potential use of nanoparticles (NPs) as cell tracking agents in ocular cell therapy, highlighting their advantages over other labeling methods such as fluorescent reporters and DNA barcoding. Two classes of NP—gold nanoparticles (GNPs) and superparamagnetic iron oxide nanoparticles (SPIONs)—may be particularly well-suited for longitudinal cell tracking in the eye, owing to their safety profile and compatibility with clinical imaging modalities. To establish these NPs as viable cell trackers in human ocular cell therapy, further research should be aimed at elucidating their eye-specific imaging characteristics, safety, and clearance. Our ability to accurately assess the critical processes in ocular cell transplantation—delivery, distribution, immune acceptance, retention, and integration—will help accelerate the progress of regenerative medicine in the eye.