Background: In line with its increasing prevalence, pulmonary Mycobacterium avium complex (MAC) disease (MAC-PD) gives rise to substantial healthcare costs. However, there is only limited information on the costs of intersectoral reimbursement. Objectives: Inpatient and outpatient costs for diagnosing and treating pulmonary MAC-PD in Germany in accordance with standard international guidelines were calculated and their potential effects on MAC disease management in Germany were determined. Methods: Hospitalization costs were calculated by using the German diagnosis related group (G-DRG) browser, with and without inclusion of the diseases most often associated with M. avium. Separated by drug macrolide susceptibility and severity of MAC-PD, the direct medical costs of suitable therapies in the outpatient setting were determined by Monte-Carlo simulation, including all conceivable options. Results: According to our simulation, the weighted mean cost of outpatient treatment over 14 or 18 months, in either case followed by a post-treatment monitoring over 12 months, amounts to €8675.22 (95% confidence interval [CI] €8616.17 to €8734.27). Of that amount, the revenue for outpatient doctors´ services, dependent on treatment duration, is low, ranging between €894.79 (10.3%) and €979.42 (11.3%), accordingly. Mean drug costs for MAC-PD patients amount to €6130.25 [95% CI €6073.52 to €6186.98], i.e., more than two third (70.7%) of the total outpatient costs. In contrast, the non-surgical reimbursement for a hospital stay of up to 14 days is €3321.64. Hospital reimbursement does not increase in cases of complications (a higher number and/or challenging type of associated diseases), but it is fully paid even in cases that require as few as 2 days of hospitalization. Conclusion: The imbalance between well-rewarded hospital care and the low reimbursement for long-term treatment of MAC-PD outpatients may induce inappropriate disease management. In order to arrive at properly integrated care of MAC-PD patients in Germany, measures such as better incentives for physicians in the outpatient setting and a targeted use of resources in hospitals are required. Reimbursed, periodic case conferences between outpatient physicians and experts in hospitals as well as preventive short-term checks of MAC-PD patients in specialty clinics may promote cross-sector cooperation and improve overall treatment quality. Nationwide pilot studies are required to gain evidence on the effectiveness of the new approach.