BACKGROUND: Post-COVID-19 syndrome (PCS) presents in a multitude of ways, with fatigue, physical constraints, and diminished quality of life being common symptoms. It is becoming increasingly clear that unimodal behavioral interventions do benefit all PCS patients. Adherence to and response to isolated psychotherapy or physical activity interventions vary greatly, with certain patients benefit more from one form of therapy, or even a combination, than others do. The study aims to compare the effects of a single exercise therapy, psychotherapy, and a combination of both therapies. METHODS: The study will be conducted as a prospective, randomized controlled, open-label trial with 3 treatment arms (exercise therapy, psychotherapy, and combined therapy). According to the sample size calculation, 65 participants will be enrolled in each group. The primary outcome is the change of PCS fatigue symptoms from baseline to 3 months, estimated by the Fatigue Assessment Scale. Secondary endpoints include changes in further measures of fatigue (Chalder Fatigue Skala, Multidimensional Fatigue Inventory, Post-exertional Malaise Scale, Bell Scale), health-related quality of life (Short Form-36 and Brief Illness Perception Questionnaire), anxiety and depression (Hospital Anxiety and Depression Scale), and work ability (Work Ability Index). The intervention lasts for 3 months and includes online therapy sessions of 50 min every 2 weeks or in case of lack of concentration or fatigue this could be split to two 25-min sessions (all equating to a total of 300 min of specialist care). The psychotherapy adopts a short-term and coping-oriented approach based on the unique requirements of each patient from a psychotherapeutic perspective. Exercise therapy involves a personalized physical activity plan customized to suit the patient's requirements, with tracking day-to-day physical activity along with daily moderate endurance and strengthening workouts. An ANCOVA model, including the stratification factors sex and BMI, will be used for the primary analysis of Fatigue Assessment Scale. Significance tests will be based on the group differences in least square means and corresponding 95% CIs. DISCUSSION: Due to the current relevance of the issue, the unclear evidence so far, and the lack of appropriately powered randomized studies, it is crucial to assess potentially effective concepts for treating patients with PCS. Future therapy decisions will benefit from answering the question of whether combined therapies hold a significant advantage over unimodal therapeutic approaches, as well as identifying predictors that indicate an advantage of certain therapies for particular patients. TRIAL REGISTRATION: ClinicalTrials.gov NCT06042751 . Registered on 21 September 2023.