Oral mucositis is the inflammation of the mucosa of the oral cavity. It is a frequent complication of cancer chemotherapy and radiotherapy. Approximately 20–40% of patients undergoing chemotherapy suffer from oral mucositis. It is very painful, impairs eating, drinking, and quality of life. One of the most effective yet simple measures to prevent and treat oral mucositis is oral care with mouthwash. Ectoine is a natural substance that was discovered in halophilic (salt-loving) bacteria. Ectoine can protect these bacteria against dehydration because it can attract water molecules and strengthen biological membranes. Ectoine is used to treat many diseases caused by allergens, UV light, air pollution, heat, and dryness. Ectoine (Ectoin®) mouthwash is produced by bitop AG (Dortmund, Germany) to treat dry mouth and other symptoms of inflamed oral mucosa. This study investigated ectoine mouthwash for the treatment of oral mucositis following chemotherapy. It was compared to the local standard-of-care calcium phosphate mouthwash. One group of patients was treated with ectoine mouthwash and the other with calcium phosphate mouthwash. After 14 days, mucositis symptoms were substantially reduced in both groups. After 21 days, all patients were almost cured of oral mucositis. Additionally, after the treatment, patients rated how effective and tolerable the treatment was. Here, more patients treated with ectoine rated their treatment as effective and tolerable than those treated with calcium phosphate. This study shows that ectoine mouthwash is tolerable and effective for the treatment of mucositis. Patients preferred ectoine mouthwash to calcium phosphate mouthwash.