Objects To evaluate prognostic factors and treatment outcomes of primary squamous cell carcinoma in thyroid (PSCCTh) over the past decades using a large national database. Methods All patients diagnosed with PSCCTh between 1973 and 2015 were identified with the Surveillance, Epidemiology, and End Results Program (SEER) 18-registry database. Relevant clinical data were collected, and prognostic factors of overall survival (OS) and disease-specific survival (DSS) were analyzed. Results This cohort study included 242 patients, accounting for 0.12% of all primary thyroid carcinomas from 1973 to 2015 nationwide. Of the patients with PSCCTh, 75% were older than 60 years at diagnosis. Patient age older than 60 years (HR 2.242, 95% CI 1.367–3.676, P  = 0.001) and a tumor size larger than or equal to 50 mm (HR 1.479, 95% CI 1.011–2.165, P  = 0.044) were independent negative prognostic factors. The univariate analysis suggested that the morphological subtype (OS, P  = 0.033; DSS, P  = 0.048), clinical treatment modality (OS, P  < 0.0001; DSS, P  < 0.0001), and T stage (OS, P  = 0.004; DSS, P  = 0.001) were important predictive factors for OS and DSS. In contrast, gender, race, year of diagnosis, geographic location, N stage, and M stage were not prognostic factors. Conclusions PSCCTh is a rare malignancy with an aggressive nature and poor prognosis. Survival is predicted by the treatment modality, patient age, T stage, tumor size, and morphological subtypes. This study showed that early diagnosis and complete surgical resection plus adjuvant radiation therapy were associated with a better outcome.