The role of microbiome, particularly Fusobacterium nucleatum (Fn), in periodontal disease and oral squamous cell carcinoma (OSCC) has been recently explored. This study aimed to evaluate the Fn presence and its levels in oral rinse samples from Brazilian OSCC patients and healthy individuals and its association with sociodemographic, clinical, and oral health features. In this case-control study, 80 participants were included, 31 OSCC patients and 49 individuals without a cancer history. Clinical data were collected, and an oral exam was done on a subset of the cohort. Fn levels were evaluated by droplet digital PCR (ddPCR) in oral rinse samples and were categorized as Fn-high or Fn-low based on the median number of copies per reaction. OSCC patients showed higher levels of Fn (68%, p = 0.03) than controls, and all OSCC cases were diagnosed with periodontal disease (100%, p = 1.0). In the univariate analysis, Fn-high level was more frequently present in OSCC cases compared to controls (p = 0.01). It was also observed that Fn-high level OSCC cases were significantly associated with self-reported non-white ethnicity (71.4%, p = 0.01) and had more infiltrative lesions (57.1%, p = 0.02) than Fn-low OSCC cases. Fn-high levels in oral rinse samples, were significantly more prevalent among OSCC than in controls. In OSCC patients, Fn-high levels were associated with non-white ethnicity and lesions with infiltrative clinical aspects. Among OSCC cases, all had periodontal disease.