Objective The retinal toxicity of intravitreal ganciclovir (GCV) is contentious. Our study aims to describe new clinical findings following intravitreal GCV and propose a mechanism for the pathogenesis of those post-injection retinal changes. Methods A retrospective case series included 114 patients with cytomegalovirus retinitis (CMVR) receiving intravitreal GCV (2.5 mg/0.05 mL) combined with systemic therapy. Patients with presumed retinal toxicity following intravitreal GCV injection were enrolled. Clinical data, laboratory tests, ocular examination, and multimodal images of the retina were collected. Serial optical coherence tomography (OCT) was performed to monitor pre- and post-retinal changes. Results Five patients (7 eyes) (4.4%+/- 2.6%) with macular spared from CMVR lesions experienced acute vision loss and transient macular edema after the GCV injection; 1 patient (0.9%+/- 2.6%) with bilateral CMVR developed chronic and progressive retinal pigment epithelium (RPE) atrophy in the CMVR-spared areas of the eye receiving repeated GCV injections, contrasting with untreated contralateral eyes. Three of them were additionally diagnosed as cytomegalovirus-immune recovery retinitis. With OCT, all eyes showed intact Bruch's membrane and normal thickness of inner retinal layers. Seven eyes with acute vision loss showed outer retinal changes within 24 h post-injection, including macular SRF (7 eyes), macular vertical hyperreflective foci (5 eyes), and ONL edema (4 eyes), and resolving spontaneously weeks later. Conclusions Intravitreal GCV treatment may trigger acute macular edema and chronic RPE degeneration in CMVR patients. We hypothesize that RPE dysfunction is the pivotal pathogenic mechanism, potentially induced by multifactorial interplay, including chemical irritation, cumulative exposure, systemic comorbidities, and ocular inflammatory cascades.