The term chronic critical illness describes patients suffering from persistent organ dysfunction and prolonged mechanical ventilation. In severe cases, COVID-19 led to chronic critical illness. As this population was hardly investigated, we evaluated the health-related quality of life, physical, and mental health of chronically critically ill COVID-19 patients. In this prospective cohort study, measurements were conducted on admission to and at discharge from inpatient neurorehabilitation and 3, 6, and 12 months after discharge. We included 97 patients (61 ± 12 years, 31% women) with chronic critical illness; all patients required mechanical ventilation. The median duration of ICU-treatment was 52 (interquartile range 36–71) days, the median duration of mechanical ventilation was 39 (22–55) days. Prevalences of fatigue, anxiety, and depression increased over time, especially between discharge and 3 months post-discharge and remained high until 12 months post-discharge. Accordingly, health-related quality of life was limited without noteworthy improvement (EQ-5D–5L: 0.63 ± 0.33). Overall, the burden of symptoms was high, even one year after discharge (fatigue 55%, anxiety 42%, depression 40%, problems with usual activities 77%, pain/discomfort 84%). Therefore, patients with chronic critical illness should receive attention regarding treatment after discharge with a special focus on mental well-being.Trial registration: German Clinical Trials Register, DRKS00025606. Registered 21 June 2021—Retrospectively registered, https://drks.de/search/de/trial/DRKS00025606.