At least 65 million people suffer from long COVID. Treatment guidelines are unclear, especially pertaining to recommendations of increased activity. This longitudinal study evaluated safety, changes in functional level and sick leave following a concentrated rehabilitation program for patients with long COVID. Seventy-eight patients (19–67 years) participated in a 3-day micro-choice based rehabilitation program with 7-day and 3-month follow-up. Fatigue, functional levels, sick leave, dyspnea and exercise capacity were assessed. No adverse events were reported and 97.4% completed the rehabilitation. Fatigue measured with Chalder Fatigue Questionnaire decreased at 7-days [mean difference (MD = − 4.5, 95% CI − 5.5 to − 3.4) and 3-month (MD = − 5.5, 95% CI − 6.7 to − 4.3). Sick leave rates and dyspnea were reduced (p < 0.001) and exercise capacity and functional level increased (p < 0.001) at 3-month follow-up regardless of severity of fatigue at baseline. Micro-choice based concentrated rehabilitation for patients with long COVID was safe, highly acceptable and showed rapid improvements in fatigue and functional levels, sustaining over time. Even though this is a quasi-experimental study, the findings are of importance addressing the tremendous challenges of disability due to long COVID. Our results are also highly relevant for patients, as they provide the base for an optimistic outlook and evidence supported reason for hope.