Removing invasive rats from islands is a powerful conservation tool, and practitioners are now targeting larger islands for rat eradication. As they do so, they face the challenge of mitigating for potential non-target impacts on native biodiversity that may be susceptible to rodenticides. We report on the eradication of black rats Rattus rattus from Anacapa Island, California, in 2001–2002, which was the first-ever invasive rodent eradication from an entire island where an endemic rodent was present and the first aerial application of a rodenticide in North America. As a mitigation strategy we staggered the rodenticide application over 2 years and held a representative sample of the Anacapa deer mouse Peromyscus maniculatus anacapae in captivity. We also mitigated for bird species potentially susceptible to brodifacoum poisoning and monitored aspects of the terrestrial and marine environments. The free-ranging native rodent population severely declined following rodenticide applications but reintroduction and translocation efforts were successful, and the population quickly recovered to pre-eradication levels. Non-target impacts also included mortality of raptors, gulls and passerines, including high mortality of rufous-crowned sparrows Aimophila ruficeps obscura despite planned mitigation. All observed non-target impacts are expected to be ephemeral; however, further monitoring should reveal details on the dynamics of those impacts. Brodifacoum was not detected in the marine environment or in significant amounts in terrestrial soil, plants and arthropods. Seabird benefits from the rat eradication were quickly realized.