A small subpopulation of cancer stem-like cells (CSCs) present in almost all tumors is responsible for drug resistance and tumor recurrence. The role of NF-kB and miRNA in close association with essential risk factors, tobacco, alcohol and high risk HPV infection during oral carcinogenesis and its prognosis is not well understood. We have isolated cancer stem like SP cells from both HPV+/-ve oral squamous cell carcinoma (OSCC) cell lines and primary tumors, which formed orospheres, expressed stemness markers Oct4, Sox-2, CD133 and CD117. These cells showed differentially upregulated expression of NF-kB proteins and selective overexpression of viral oncogenes E6/E7 only in HPV16+ve cells which formed higher number of orospheres, overexpressed c-Rel and selectively activated p65 that heterodimerized with p50 to show higher DNA binding activity. Further, selective over expression of miR-21 and miR-155 and downregulation of miR-34a were demonstrated by HPV+ve CSCs which overexpress HPV16 oncogene E6 that is responsible for the maintenance of stemness. While, HPV-ve CSCs show exclusively p50 homodimeriztion, poor differentiation and worst prognosis, HPV infection induced participation of p65 along with deregulated expression of specific miRNAs led to well differentiation of tumors and better prognosis.