BACKGROUND: The fat mass and obesity-associated protein (FTO) is implicated in various diseases and acts as a demethylase for the most abundant modification of mRNA, namely N6-methyladenosine (m6A) modification. It is known that FTO may play an oncogenic role or a tumor-suppressor role in different malignancies. The aim of this study was to investigate the functional roles of FTO in regulating biological processes related to hypopharyngeal squamous cell carcinoma (HSCC). METHODS: Using immunohistochemistry, quantitative real-time polymerase chain reaction (RT-qPCR), and Western blot analysis, we compared the expression levels of FTO in HSCC tissues to adjacent non-cancerous tissues. Furthermore, we evaluated the prognosis of patients with hypopharyngeal cancer in relation to FTO expression levels. In vitro, the Cell Counting Kit-8 (CCK8), wound healing assay, migration and invasion assays were used to identify roles of FTO in HSCC cells FaDu. Tumor xenografts in nude mice were used to disclose the effect of FTO in vivo. Then, transcriptome RNA sequencing (RNA-seq) assays were applied to screen for possible target genes. To confirm the specific site for modulating the expression of the target gene, we used the SRAMP database and methylated RNA immunoprecipitation PCR (MeRIP-PCR). RESULTS: The results showed that FTO was highly expressed in hypopharyngeal cancer tissues and was correlated with clinicopathology of patients. FTO promoted the proliferation, invasion and migration of hypopharyngeal cancer cells in vitro through its demethylase action. In vivo experiments showed that FTO promoted the growth of subcutaneously implanted tumors of hypopharyngeal cancer cells and their metastasis. Moreover, we revealed that FTO affected the malignant biological behavior of hypopharyngeal cancer cells by regulating the m6A modification level of SERPINE1 mRNA. FTO promoted epithelial-mesenchymal transformation (EMT) of hypopharyngeal cancer cells through the SERPINE1 signaling axis. CONCLUSIONS: Our study highlighted the functional significance of the FTO/SERPINE1 axis in tumorigenesis of HSCC. Targeting FTO holds promise as a new therapeutic strategy for HSCC.