Certain cancers exhibit unique expression profiles of small nucleolar RNAs (snoRNAs), and the aberrant expression of snoRNAs may play significant roles in tumor biology. As the most common endocrine malignancy, the expression pattern and clinical relevance of snoRNAs in papillary thyroid carcinoma (PTC) remain largely unexplored. In this study, we employed small RNA microarray analysis to profile snoRNA expression in tumor tissues and corresponding normal thyroid tissues obtained from patients undergoing thyroidectomy. Differentially expressed snoRNAs (DE-snoRNAs) were validated by quantitative real-time PCR (qRT-PCR) and analysis of The Cancer Genome Atlas (TCGA) database. Furthermore, we applied CIBERSORTx and ESTIMATE algorithms to investigate the association between DE-snoRNA expression levels and clinicopathological features as well as tumor immune microenvironment in PTC. Our results revealed that SNORA68B, SNORA70F, and SNORD88A were downregulated in PTC tissues and potentially associated with the composition and distribution of tumor-infiltrating immune cells.