Moyamoya disease (MMD) is a rare chronic cerebrovascular disease mainly found in individuals of East Asian ethnicity, and its pathogenesis is largely unknown. Transfer RNA-derived fragments (tRFs) are novel biological entities involved in many biological processes; however, whether tRFs contribute towards MMD pathogenesis remains unexplored. In the present study, deep sequencing technology was used to identify alterations in tRF expression profiles between patients with MMD and healthy controls. The sequencing findings were validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Subsequently, the putative target genes of tRFs were predicted using miRNA target prediction algorithms. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to further evaluate potential functions of tRFs. The sequencing results demonstrated that 38 tRFs were differentially expressed between patients and controls, of which 22 were upregulated and 16 were downregulated. RT-qPCR analysis confirmed the validity of the sequencing results. GO and KEGG pathway enrichment analyses indicated that 15 pathways were associated with the selected tRFs. These pathways were mainly involved in angiogenesis and metabolism, both of which are physiopathological fundamentals of MMD. The results provided a novel insight into the mechanisms underlying MMD pathogenesis, and demonstrated that tRFs may serve as potential therapeutic targets for the future treatment of MMD.