Background: Prognostic uncertainty can be a barrier to providing palliative care. Accurate prognostic estimation in patients at the end of life is a challenging issue.Methods: A retrospective longitudinal observational study was conducted collaborated by three medical facilities in a rural super-aged community in Japan. We established a unique end-of-life diagnostic process consisting of (1) physicians’ judgement, (2) disclosure to patients, and (3) discussions at an end-of-life case conference (EOL-CC), which were based on Japanese end-of-life related guidelines. Participants were consecutive patients discussed at EOL-CC between January 1, 2010, and September 30, 2017. The primary study outcome was mortality within 6 months after the initial EOL-CC decision. The secondary outcome was diagnostic odds ratio using EOL-CC diagnosis (end-of-life or non-end-of-life) as an index test and overall survival (less than 6 months or 6 months and more) as a reference standard.Results: A total of 315 patients were eligible for survival analysis (189 women, median [range] age 89 [54–107] years). In the survival analysis, end-of-life diagnosis was associated with much lower survival rate at 6 months after EOL-CC than non-end-of-life diagnosis (6.9% vs 43.5%, respectively; P < 0.001). However, 10 of the end-of-life patients were alive more than 1 year later (maximum 6.3 years). Of participants, 297 were eligible for diagnostic accuracy analysis (165 women, age 89 [54–107] years). The EOL-CC diagnosis showed high sensitivity (0.95; 95% CI 0.92–0.97) but low specificity (0.35; 95% CI 0.20–0.53) against the outcomes. It also showed the highest negative predictive value (0.44; 95% CI 0.23–0.64), the lowest negative likelihood ratio (0.14; 95% CI 0.07–0.29), and the highest diagnostic odds ratio (10.32; 95% CI 4.08–26.13) compared with other prognostic prediction tools (Charlson Comorbidity Index, Palliative Performance Scale, and Advanced Dementia Prognostic Tool).Conclusions: The diagnostic process using the Japanese end-of-life guidelines enabled more accurate identification and prognostication of end of life than existing prognostic tools. However, the study population was limited to patients with severe conditions, thus further research is necessary to build full consensus.