Objective The aim of this study was to formulate a retrospective study investigating the ocular findings and associated risk factors in long-term survivors after allogenic-hematopoietic stem cell transplantation (HSCT) in Saudi Arabia. Patients and methods This observational study was conducted on patients who underwent HSCT from 1996 to 2016 at King Faisal Specialist Hospital and Research Center in Riyadh, Saudi Arabia. The study included 72 patients who were human leukocyte antigen-matched donors with identical matched sibling donors. Peripheral blood was the source of stem cells in 61 patients. The ophthalmological examination included visual acuity (VA) testing, refraction, tear break-up time, Schirmer’s test, slit-lamp biomicroscopy, and dilated ophthalmoscopy. Chronic ocular graft-versus-host disease (GVHD) inclusion was based on strict selection criteria. The patients identified with mild to moderate ocular GVHD had less than or equal to three corneal staining, 13–32 points ocular surface disease index (OSDI), and Schirmer’s test of 6–15 mm were classified as group 1, while those with severe ocular GVHD defined as having more than four corneal stainings, more than or equal to 33 points OSDI, and less than or equal to 5 mm Schirmer’s test were classified as group 2. Impairment of VA was classified as mild (20/22–20/50), moderate (20/70–>20/200), or severe (≤20/200) impairment. Results Chronic GVHD was diagnosed in 394 patients within the first 5 years after transplantation. Ocular GVHD was detected in 81 (20.56%) patients. They were classified into group 1 (65 patients, 80.25%) with mild to moderate ocular GVHD and group 2 (16 patients, 19.75%) with severe ocular GVHD. All patients had OSDI ranging from more than or equal to 13 to more than or equal to 33. Retinal changes were detected in five patients, optic disc changes in two patients, steroid-induced proliferative diabetic retinopathy in three patients, and old branch retinal vein occlusion in one patient. All patients with identical matched sibling donor showed normal or mild to moderate impaired VA except for two patients. All patients responded to topical eye drops except for nine who required surgical procedures. Normal or mild impaired VA was reported in 59 patients with statistical significance (P=0.0053), while 42 male patients versus 29 females had normal or mild impaired VA with a statistically significant difference (P=0.0179). Conclusion Ocular GVHD is a complex disease in our unique population. Every patient before allogenic HSCT be referred to a cornea specialist to evaluate the baseline parameters for the pre-HSCT diagnosis of dry eye disease.