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Background and objectives Despite a high incidence of hypopharyngeal cancer in northeast India, the role of dietary patterns and meal timing remains poorly understood. This study examined the association between inter-meal intervals, dietary patterns, and the risk of hypopharyngeal cancer in northeastern India. Methods A hospital-based case-control study was conducted at a tertiary cancer centre in northeastern India, enrolling 300 histologically confirmed cases with hypopharyngeal cancer and 300 frequency-matched controls between May 2023 and August 2024. Dietary intake and inter-meal intervals were assessed using a semi-quantitative food frequency questionnaire. Multivariable logistic regression calculated odds ratios and 95% confidence intervals, adjusting for demographics, socioeconomic status, alcohol consumption, smoking, and tobacco use, including areca nut consumption. Results Prolonged inter-meal intervals (≥5 h) conferred a nearly three-fold increased risk of hypopharyngeal cancer compared to intervals <4 h [adjusted odds ratio (OR) 2.69, 95% confidence interval (CI): 1.56-4.69]. Strong protective effects emerged for citrus fruits (highest tertile OR 0.13, 95% CI: 0.05-0.32) and leafy green vegetables (highest tertile OR 0.21, 95% CI: 0.09-0.49). Coffee consumption was inversely associated with the risk of hypopharyngeal cancer (OR 0.54, 95% CI: 0.30-0.94), while higher milk intake increased the risk of hypopharyngeal cancer (OR 2.06, 95% CI: 1.22-3.52). Interpretation and conclusions We provide epidemiological evidence linking prolonged inter-meal intervals to the risk of hypopharyngeal carcinoma in an Indian population. Meal timing patterns may be as important as dietary composition for cancer prevention, with implications for public health interventions in high-risk populations.