AXL expression and activation confer resistance to multiple anti-cancer agents including of inhibition of the Phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K), thus uncovering the molecular mechanism that regulates AXL expression in cancer cells is urgently needed. In this work, we demonstrated that AXL expression levels determine the sensitivity of the isoform-specific inhibitors of the PI3K, BYL719, in the human papillomavirus positive and negative (HPVpos and HPVneg) head and neck and esophageal squamous cell carcinoma cell lines (HNCC and ESCC) in vitro and in vivo. AXL expression is regulated by the AP-1 transcription factor, as knockdown of AP-1 members (c-JUN and FOS) resulted in the reduction of AXL expression, which was concomitant with enhancing sensitivity to BYL719 in vitro. The association in the expression of AXL and c-JUN was validated in 17 HPVpos and HPVneg HNC and ESCC cell lines, and in three independent cohorts of head and neck cancer patients, and in patient-derived xenografts. Pharmacological inhibition of the c-Jun N-terminal kinase, JNK, using SP600125 had additive or synergistic anti-tumor activity against most PIK3CA- mutated and HPVpos tumor cells lines in vitro when combined with BYL719. In vivo, the efficacy of drug combination showed a potent anti-tumor activity in two HNC cell lines, two patient-derived xenografts, and in two syngenic HNSCC murine models. A significant reduction of tumor cell proliferation and further inhibition of mTOR was observed when mice treated with a combination of SP600125 and BYL719 compared to a single agent. Collectively, our data suggest that AXL is transcriptionally regulated by AP-1, and reducing its expression using JNK inhibitors is a new therapeutic strategy that needed to be tested in patients with HPVpos or PIK3CA-mutated HNSCC and ESCC patients.