Strong prognostic biomarkers are lacking regarding the stratification of treatment and surveillance regimens in head and neck squamous cell carcinoma (HNSCC). The study aimed to assess the prognostic value of soluble urokinase-type plasminogen activator receptor in plasma (suPAR) compared to evaluation by uPAR-positron-emission-tomography (PET) in HNSCC patients. Plasma from 19 controls and 49 HNSCC patients referred to curatively intended radiotherapy (2017–2021) was collected pre-treatment and post-treatment (n = 37). Information on uPAR-PET was available from previous evaluation. Patient median suPAR was significantly higher pre- and post-treatment compared to controls (p = 0.013, p = 0.003) and increased significantly during radiotherapy (p = 0.003). Pre-treatment suPAR did not predict survival outcomes. Post-treatment suPAR significantly predicted RFS (HR = 6.67 (95% CI 1.44–30.9) p = 0.015), but not OS (HR = 3.29 (95% CI 0.882–12.3) p = 0.076) in univariate analysis. RFS prediction was maintained for post-treatment suPAR in multivariate analysis, including TNM-stage (HR = 6.62 (95% CI 1.40–31.4) p = 0.017). Pre-treatment uPAR-PET/CT and post-treatment suPAR was available in 24 patients. High uPAR-estimates on both modalities was significantly associated with poor RFS compared to patients with low uPAR-estimates (log-rank, p = 0.008). Patients with discordant uPAR-estimates (one-low/one-high) were at intermediate risk, although non-significant (p = 0.131). In conclusion, pre-treatment suPAR did not predict RFS or OS. Pre-treatment uPAR-PET and post-treatment suPAR predicted RFS.