Thyroid-like low-grade nasopharyngeal papillary adenocarcinoma (TLLG-NPPA) is a distinctly rare malignancy of the nasopharynx. Morphologically and immunophenotypically, TLLG-NPPA resembles papillary thyroid carcinoma (PTC) and is characterized by a papillary architecture with PTC-like nuclear features and thyroid transcription factor-1 expression. Recently, some cases of TLLG-NPPA with a spindle cell component have been reported. In this study, we report a very interesting case of biphasic TLLG-NPPA that was predominantly composed of spindle cells, with comprehensive analyses of its clinical, pathological, and immunophenotypical features. A 50-year-old woman presented with a sensation of a foreign body in the nasopharynx. Nasopharyngoscopy and computed tomography demonstrated a pedunculated mass arising from the nasopharyngeal roof. Based on the clinical impression of a nasopharyngeal tumor, an excisional biopsy was performed. At low-power magnification, the nasopharyngeal mass consisted of papillary tumor tissue, the growth pattern and architecture of which resembled those of PTC. The papillae were complex and packed tightly with fibrovascular cores. At high-power magnification, each papillary structure was lined with a pseudostratified cuboidal-to-columnar epithelium. The tumor cell nuclei frequently showed a ground-glass appearance, intranuclear grooves, pseudoinclusions, and membrane thickening and irregularity, resembling the characteristic nuclear morphology of PTC. These histological features were compatible with TLLG-NPPA. Intriguingly, in between the papillary components were spindle cells that appeared very similar to the glandular epithelial cells that imperceptibly merged with the papillary component. This spindle cell component comprised two-thirds of the entire tumor volume. The nuclear morphology of the spindle cell component was similar to that of the papillary component. On immunostaining, both the papillary and spindle cell components were diffusely and strongly positive for thyroid transcription factor-1, cytokeratin 7, cytokeratin 19, vimentin, and Hector Battifora mesothelial-1. In contrast, the tumor cells tested negative for p63, p40, smooth muscle actin, S-100, cytokeratin 5/6, thyroglobulin, BRAF V600E, and Epstein–Barr virus-encoded small RNAs. Only two cases of biphasic TLLG-NPPA exhibiting a prominent spindle cell component had been reported previously in the English literature. When the pathologist receives a primary nasopharyngeal mass with the aforementioned histological features, particularly biopsy specimens with predominant spindle cells, biphasic TLLG-NPPA should be considered in the differential diagnosis. By describing its detailed clinicopathological characteristics, we anticipate that this report will expand the existing knowledge on the spindle cell component associated with TLLG-NPPA.