Background/Objectives: The physical performance and functional status of individuals with long COVID may be altered. Health resort treatment comprises balneology, exercises, physical medicine modalities, and climate therapy. Complex treatment in a sanatorium may have a positive effect on long COVID patients. This study assessed functional status, physical performance, and fatigue in people with long COVID that qualified for the health resort treatment and its efficacy in this group of patients. Methods: A retrospective review of the medical records of 116 patients (66 women and 50 men) undergoing health resort treatment for long COVID in 2021 at the Rehabilitation Hospital and Sanatorium “Gwarek” in Goczałkowice-Zdrój (Poland) was conducted. Data were collected between March and May 2024. Their functional status, physical performance, and level of fatigue were assessed twice: before and after the treatment. Results: After the health resort treatment, their physical performance (10.41 points ± 1.84 points vs. 11.57 points ± 0.94 points; p < 0.00001) and functional status (2.13 points ± 0.88 points vs. 1.23 points ± 0.62 points; p < 0.00001) improved. Their fatigue (4.83 points ± 2.38 points vs. 2.15 points ± 1.31 points; p < 0.00001) level was diminished after the treatment. Conclusions: Fatigue was of moderate intensity in the long COVID patients that qualified for the health resort treatment. Most of the long COVID patients reported mild functional limitations, whereas their physical performance was undisturbed. Health resort treatment improved functioning in patients with persistent COVID-19 symptoms by reducing fatigue, improving their functional capacity and physical performance. It should be recommended as a supplement to the standard treatment because of its complexity.