Background: Geriatric health service facilities (GHSFs) play important roles as intermediate care facilities for elderly individuals temporarily when they need rehabilitation before returning home. However, the number of residents spending their end-of-life (EOL) period in such facilities is increasing. To improve the quality of EOL care, end-of-life discussions (EOLDs) are recommended by some guidelines and studies. Aim: This study aimed to clarify the current practice of EOL care and EOLDs in GHSFs in Japan. Methods: We conducted a nationwide cross-sectional survey by mailing questionnaires about EOL care and EOLDs to 3437 GHSF managing directors. The questionnaire was developed through a literature review and discussion among the researchers and experts. Descriptive statistics summarized the data. We also analyzed the factors related to GHSFs conducting EOLDs using Fisher exact tests. Results: The response rate was 20.7% (713 of 3437). Among the respondents, 75.2% (536 of 713) of GHSFs provided EOL care and 73.1% (521 of 713) conducted EOLDs. The most common reasons for difficulties in providing EOL care included the lack of EOL education for nurses and care workers, and their fear about caring for dying residents. End-of-life discussions were mostly initiated after the deterioration of a resident’s condition and were conducted with families by physicians. Statistically significant factors of GHSFs conducting EOLDs included providing EOL education for nurses and care workers, availability of private room for critically ill residents, emergency on-call doctors, and EOL care. Conclusion: Adequate practical staff education programs for EOL care including EOLDs may be crucial for quality of end-of-life care in aged care facilities.