Head and Neck Squamous Cell Carcinomas (HNSCC) are characterized by a large heterogeneity in terms of the location and risk factors. For a few years now, immunotherapy seems to be a promising approach in the treatment of these cancers, but a better understanding of the immune context could allow to offer a personalized treatment and thus probably increase the survival of HNSCC patients. In this context, we evaluated the infiltration of FoxP3+ Tregs on 205 human formalin-fixed paraffin-embedded HNSCC and we assessed its prognostic value compared to other potential prognostic factors, including HPV infection. First, we found a positive correlation of FoxP3+ Treg infiltration between the intra-tumoral (IT) and the stromal (ST) compartments of the tumors (p < 0.0001). A high infiltration of these cells in both compartments was associated with longer recurrence-free (ST, RFS, p = 0.007; IT, RFS, p = 0.019) and overall survivals (ST, OS, p = 0.002; ST, OS, p = 0.002) of HNSCC patients. Early tumor stage (OS, p = 0.002) and differentiated tumors (RFS, p = 0.022; OS, p = 0.043) were also associated with favorable prognoses. Multivariate analysis revealed that FoxP3+ Treg stromal infiltration, tumor stage and histological grade independently influenced patient prognosis. In conclusion, the combination of these three markers seem to be an interesting prognostic signature for HNSCC.