Background: Information on epidemiology of prolonged mechanical ventilation (PMV) patients in the acute care setting in Japan is totally lacking. We aimed to investigate clinical features, impact, and long-term outcomes of PMV patients. Methods: This was a retrospective observational study conducted in a tertiary care hospital. Adult patients who were admitted to our intensive care unit (ICU) from April 2009 to March 2014 and required mechanical ventilation (MV) for ≥ 2 days were included. PMV was defined as having MV for ≥ 21 consecutive days. Results: Among 1282 MV patients, 93 (7.3%) required PMV, and median duration of MV was 37.0 days. Compared with the non-PMV patients, PMV patients had longer total ICU and high care unit (HCU) stay (34.0 vs. 7.0 days, p < 0.001), longer hospital stay (74.0 vs. 35.0 days, p < 0.001), and higher hospital mortality (54.8 vs. 21.4%, p < 0.001). In multivariable logistic regression analysis, emergency ICU admission and steroid use during MV were associated with PMV. The Kaplan-Meier curves for MV withdrawal and ICU/HCU discharge were almost identical. Among PMV patients, 52 (55.9%) died, 29 (31.2%) were successfully liberated from MV during hospitalization, and 12 (12.9%) still required MV at discharge. Conclusion: In this investigation, 7.3% of the patients with MV required PMV. Most PMV patients were liberated from MV during hospitalization, while occupying critical care beds for an extended period. A nationwide survey is required to further elucidate the overall picture of PMV patients and to discuss whether specialized weaning centers to treat PMV patients are required in Japan.