Background: Malnutrition in oesophageal and pharyngeal cancer patients constitutes a common and serious concern, which significantly reduces patients’ prognosis. Cancers of the oesophagus and the pharynx can considerably impair feeding in patients, resulting in severe undernutrition. This is a scoping review which aims to critically summarize and scrutinize the current clinical evidence on the use and prognostic role of diverse nutritional assessment tools on the prognosis of patients with oesophageal and pharyngeal cancers. Methods: PubMed, Scopus, Web of Science and Google Scholar databases were comprehensively explored utilizing relative keywords to detect clinical studies that investigate whether nutritional status may affect disease prognosis. Results: Several assessment tools have evaluated and highlighted the prognostic role of nutritional status on patients’ survival and disease complications in both oesophageal and pharyngeal cancers. Regarding oesophageal cancer, CONUT, PNI, PG-SGA and NRS-2002 are more commonly used, while albumin is also frequently evaluated. Regarding pharyngeal cancers, fewer studies are currently available. PNI has been evaluated and its significance as a factor for shorter overall survival, distant metastasis-free survival, progression-free survival, and locoregional recurrence-free has been highlighted. Comprehensive Nutritional Index has also been evaluated with positive results, as well as NRS 2002, GPS, and body weight status. However, there is currently a lack of studies with adequate female patients. There is also a significant lack of well-designed prospective studies with well-organized methodology. Conclusion: Nutritional status may significantly affect disease progression and patients’ survival, highlighting the importance of a good nutritional status in patients with oesophageal and pharyngeal cancers. Further large-scaled and well-designed prospective clinical studies are strongly recommended to verify the potential beneficial effects of nutritional status in patients with oesophageal and pharyngeal cancers.