Indolent NK-cell lymphoproliferative disorder of the gastrointestinal tract (iNKLPD) is a newly recognized entity in the 5th edition of the World Health Organization (WHO) Classification of Haematolymphoid Tumours: Lymphoid Neoplasms. Initially described as "NK-cell enteropathy" and "lymphomatoid gastropathy" over a decade ago, recent molecular and cytogenetic studies have confirmed its neoplastic nature. Although primarily affecting the gastrointestinal tract, iNKLPD has also been reported in rare extra-intestinal sites, including the gallbladder, lymph nodes, nasopharynx, and vagina. Case presentation We present a unique case involving the nasal cavity, which has not been previously reported as a site of involvement. A 67-year-old female patient presented with recurrent postnasal drip symptoms persisting for one year following an upper respiratory tract infection. Imaging studies revealed a nasal mass on head computed tomography (CT), prompting endoscopic resection. Intraoperatively, a mulberry-like neoplasm was identified in the left nasal septum. Histopathological examination using hematoxylin-eosin (HE) staining revealed diffuse infiltration by medium to large round cells. Immunohistochemical profiling demonstrated positive expression of CD56, CD3, BCL-2, TIA-1, and Granzyme B, with a Ki-67 proliferation index of 50%. CD5, CD20, CD21, CD23, CD10, BCL-6, CD30, PAX-5, and PD-1 were negative. Notably, in situ hybridization for Epstein-Barr virus (EBV)-encoded RNA was negative, and T-cell receptor (TCR) gene rearrangement was not detected by polymerase chain reaction (PCR) analysis, confirming the diagnosis of indolent NK-cell lymphoproliferative disorder (iNKLPD) of the gastrointestinal tract. After 11 months of follow-up, the patient showed no local recurrence or signs of lymph node enlargement in other anatomical regions. Furthermore, proteomics analysis of the case was conducted in conjunction with Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Conclusion Although iNKLPD is a rare tumor, cases involving the nasal cavity are exceptionally uncommon and have not been reported in the literature. This unique case represents the first documented instance of iNKLPD in the nasal cavity, contributing to the comprehensive understanding of its pathological diagnosis and clinical management. Proteomics analysis of the case has provided valuable insights into the molecular mechanisms underlying this rare disease.