In this report, we describe a case of Rhodococcus equi lung infection diagnosed in an allogeneic hematopoietic stem cell transplant with oral graft-versus-host disease 3 months after stem cell infusion. The lung lesion persisted despite an approximate 3 months of vancomycin therapy, but then responded favorably to a combination of intravenous ertapenem at 1 g daily and oral rifampin at 600 mg daily for 1 month. An overview of Rhodococcus infection in transplant recipients is presented. This case and the discussed literature suggest that combination antibiotic therapy is warranted in patients with decreased humoral and cellular immunity.