How mutations in the non-coding U8 snoRNA cause the neurological disorder leukoencephalopathy with calcification and cysts (LCC) is poorly understood. Here we report the generation of a mutant U8 animal model for interrogating LCC-associated pathology. Mutant U8 zebrafish exhibit defective central nervous system development, a disturbance of ribosomal RNA (rRNA) biogenesis and tp53 activation, which monitors ribosome biogenesis. Further, we demonstrate that fibroblasts from LCC individuals are defective in rRNA processing. Human precursor-U8 (pre-U8) containing a 3´ extension rescued mutant U8 zebrafish, indicating conserved biological function. Analysis of LCC-associated U8 mutations in zebrafish revealed one null and one functional allele contributes to LCC. We show that mutations in three nucleotides at the 5´ end of pre-U8 alter the processing of the 3´ extension, and identify a previously unknown base-pairing interaction between the 5´ end and 3´ extension of human pre-U8. Indeed, LCC-associated mutations in any one of seven nucleotides in the 5´ end and 3´ extension alter the processing of pre-U8, and are present on a single allele in almost all LCC individuals identified to date. Given genetic data indicating that biallelic null U8 alleles are likely incompatible with human development, and that LCC is not caused by haploinsufficiency, the identification of hypomorphic misprocessing mutations that mediate viable embryogenesis furthers our understanding of LCC molecular pathology and cerebral vascular homeostasis.