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Background: Primary thyroid lymphoma (PTL) is a rare thyroid malignancy, there are few large sample studies on PTL and no standardized treatment regimen has been established due to the rarity. The aims of this study were to explore the incidence and prognostic factors of PTL and construct visual prognostic prediction models for post-chemotherapy and postoperative patients. Methods: The incidence of PTL in 1975–2017 was extracted from the US Surveillance, Epidemiology, and End Results (SEER) database, then assessed using joinpoint regression software. A total of 1616 eligible PTL patients diagnosed in 1998–2016 were brought into prognostic analysis. Multivariate Cox regression analyses were carried out to reveal independent prognostic elements for overall survival (OS) and cancer-specific survival (CSS). Results: PTL incidence showed a relatively steady increase in 1975–1994, which annual percent change (APC) was 4.0%, and steady decreasing in 1994–2017(APC − 2.4%). Age, marital status, lymphoma Ann Arbor stage, histological subtypes, surgery, chemotherapy, and radiation were significantly correlated to OS and CSS. Nomograms were constructed to predict OS and CSS in post-chemotherapy and postoperative PTL patients separately, and were verified to have good reliability. Conclusions: The incidence of PTL increased and subsequently decreased. We revealed the prognostic implications and constructed reliable nomograms for post-chemotherapy and postoperative PTL patients. [ABSTRACT FROM AUTHOR]