Background: Dyskeratosis congenita is a rare genetic disorder resulting from mutations that lead to shortened telomeres and premature cellular aging. Although it classically presents with a triad of mucocutaneous abnormalities, it has diverse clinical manifestations, affecting multiple organ systems. Neurological involvement, often seen in severe variants, constitutes a significant element of the disease’s pathophysiology, highlighting the vast array of observed complications. Case Presentation: A 5-year-old girl with a known diagnosis of dyskeratosis congenita due to a WRAP53 mutation presents with bloody stools and epilepsy. Her clinical course was marked by gastrointestinal disturbances, hematologic sequelae, and severe hepatic manifestations, including recurrent bleeding episodes. Discussion: This case highlights the complex interplay between telomere dysfunction and the systemic and neurological manifestations in dyskeratosis congenita. The serial brain MRI findings reveal progressive white matter disease, brain volume loss, and choroid plexus calcifications, indicating a rapid neurodegenerative progression and premature aging. Enhanced surveillance and tailored management strategies are crucial to mitigate disease-associated morbidity. Conclusion: Dyskeratosis congenita due to a WRAP53 mutation enriches our understanding of its neurodegenerative dimensions and emphasizes the pivotal role of telomeres in systemic and neurological health. Integrating advanced imaging with comprehensive multidisciplinary management improves disease monitoring and optimizes patient care.