Introduction Ischemia reperfusion injury (IRI) contributes to partial flap and solid organ transplant failure. Heme-oxygenase 1 (HO-1) is an inducible, cytoprotective enzyme which protects against IRI in solid organ transplant models. Heme arginate (HA), a HO-1 inducer, is a promising, translatable, preconditioning agent. This study investigated the effects of preconditioning with HA on the clinical outcome of a myocutaneous IRI model. Methodology Forty, male, Lewis rats were randomized to receive intravenous: (1) Control- NaCl; (2) HA; (3) HA and tin mesoporphyrin (SnMP), a HO-1 inhibitor; (4) SnMP alone. 24 h later an in situ transverse rectus abdominis myocutaneous (TRAM) flap was performed under isofluorane anaesthesia. Viability of flaps was measured clinically and by laser Doppler perfusion scanning. In vitro work on human epidermal keratinocytes (HEKa) assessed the effects of: HA; SnMP; the iron chelator desferrioxamine (DF) on: (1) cytotoxicity; (2) intracellular reactive oxygen species (ROS) concentration; and (3) ROS-mediated DNA damage. Results In contrast to our hypothesis, HA preconditioning produced over 30% more flap necrosis at 48 h compared with controls (p = 0.02). HA containing treatments produced significantly worse flap perfusion at all postoperative time points. In vitro work showed that HA is cytotoxic to keratinocytes. This cytotoxicity was independent of HO-1 and was mediated by the generation of reactive oxygen species by free heme. Conclusion In contrast to solid organ data, pharmacological preconditioning with HA significantly worsened clinical outcome thus indicating that this is not a viable approach in free flap research.