Primary testicular lymphoma (PTL), often appearing as focal masses in the scrotum and epididymides, is the most frequent testicular tumor in aged men. Although MYD88 and CD79B mutations were the most common genetic alterations observed, the gene mutation landscape of PTL remains poorly defined. In this study, we identified 1326 mutations involving 311 genes or regions in 90 PTL patients through next-generation sequencing (NGS). PTL patients with the TBL1XR1 mutation, irrespective of treatment therapy, had an inferior overall survival (OS) than TBL1XR1 WT (wild type) patients (p = 0.045). Moreover, patients with this mutation, treated with a CHOP regimen (CTX 750 mg/m2 iv, d1,8 ADM 50 mg/m2 iv, d1 VCR 1.4 mg/m2 iv, d1 PDN 100 mg/m2 po d1–5), had a poorer OS (p = 0.019). In addition, such patients were prone to have a more intensive infiltration of tumors (p = 0.025, x2 = 4.890). Thus, we speculated that patients with a TBL1XR1 mutation have poorer prognosis, partly due to greater invasion and infiltration of tumors. Our results suggest that the TBL1XR1 mutation can be used as an indicator to predict the prognosis of PTL and can be employed as a promising new target for treatment of PTL in the future.