Squamous cell carcinoma (SCC), a common malignancy affecting the skin, vagina, uterine cervix, anus, larynx, and upper digestive tract, is characterized by significant disruption of cell-cell adhesion in stratified squamous epithelium during tumorigenesis, progression, and metastasis. CALML5, a stratified epithelial-specific protein linked to desmosomal junctions, plays a key role in cell adhesion and is notably downregulated in human papillomavirus (HPV)-associated cervical SCC. Esophageal and pharyngeal cancers, commonly with a squamous cell phenotype, have distinct etiologies: oropharyngeal carcinoma is strongly associated with HPV, whereas esophageal carcinoma is linked to environmental factors such as smoking, alcohol, and diet. To investigate the role of CALML5 in these cancers, we performed immunohistochemical analyses on clinical samples and explored its regulatory mechanisms using studies with human esophageal SCC cell lines. Our findings revealed that CALML5 expression is suppressed in early-stage esophageal SCC but reactivated at invasive sites in well to moderately differentiated SCC undergoing keratinization. In specialized SCC with sarcomatoid component, CALML5 reactivation occurred alongside aberrant KLF4 expression, highlighting its context-dependent role in tumor progression. Conversely, while HPV-unrelated oropharyngeal SCC exhibited patterns similar to esophageal SCC, HPV-related oropharyngeal SCC consistently showed suppressed CALML5 expression due to impaired KLF4 nuclear translocation. These results suggest that CALML5 functions as a tumor suppressor in HPV-associated cervical SCC but may be reactivated in non-HPV-associated invasive SCC, emphasizing its complex role in SCC pathogenesis and the need for careful interpretation of its expression in clinical contexts.