Rhodococcus equi (R. equi) is a soil-dwelling bacterium that is increasingly associated with pulmonary infections in immunocompromised patients. While antibiotic therapy remains the cornerstone of treatment, surgery combined with antibiotics has an important role in select cases. We report two cases of pulmonary R. equi in immunocompromised patients who were treated with antibiotics, followed by surgical resection of the infected tissues, and then long-term antibiotics. Both patients had excellent outcomes. We advocate surgical resection of grossly infected pulmonary tissue as an adjunct to antimicrobial therapy for treatment of this uncommon, but potentially lethal pathogen.