Background: Chorioretinal folds are observed after vitrectomy due to ocular collapse caused by low intraocular pressure. The purpose of this study is to investigate the relationship between the postoperative hypotony, chorioretinal folds, and the fundus autofluorescence (FAF) findings. Methods: Two-hundred-and-seventy consecutive eyes that had undergone 25- or 27-gauge vitrectomy were examined. The associations between the arch-shaped hypo-autofluorescent lesions in the FAF images and the postoperative hypotony with intraocular pressure (IOP) ≤ 4 mmHg were determined on the day after the surgery. Results: Arch-shaped hypo-autofluorescent lesions were seen in 4 of the 270 eyes (1.5%), and hypo-autofluorescence was observed in 3 of 14 hypotonic eyes (18.5%). This was significantly more frequent than in the non-hypotony group (0.4%, p = 0.0004). Optical coherence tomography showed a loss of the ellipsoid zone and retinal pigment epithelial layer in the region of the arch-shaped lesions. None of the arch-shaped hypo-autofluorescent lesions involved the fovea, and the vision recovered in all cases. The hypo-autofluorescent lesions did not disappear during the 4 to 16 month observation period. Conclusions: The postoperative arch-shaped hypo-autofluorescent lesions were associated with postoperative hypotony and RPE damage due to chorioretinal folds. These findings remained even when the IOP was normalized and chorioretinal folds disappeared.