Pulmonary atypical mycobacteriosis is a refractory pulmonary disease that has become resistant to the commonly used medicines. Here we report a case in which shakanzoto with yokuinin was useful in the treatment of bloody sputum caused by pulmonary atypical mycobacteriosis through Mycobacterium avium complex infection. An 86-year-old woman was diagnosed with pulmonary atypical mycobacteriosis four years before hospital admission because of repeated incidents of bloody sputum that had been unsuccessfully treated with stypsis. We administered shakanzoto with yokuinin, after which the bloody sputum disappeared rapidly. Although shakanzoto is usually prescribed for arrhythmia and cardioneurosis, our results suggest that shakanzoto is also useful for pulmonary diseases in which the pulse rate is irregular.