Control of scabies based on treatment of individual cases is difficult because of frequent re-infestation. We implemented a community intervention trial of mass drug administration (MDA) for scabies to ascertain the efficacy and safety of two alternative regimens (topical permethrin and oral ivermectin MDA), compared with standard care. We identified three isolated island communities in Fiji and randomly assigned one of the three treatment regimens: ivermectin MDA, permethrin MDA or standard care with permethrin. All participants were sought for re-examination at 12 months, and at 24 months via a 20% sample. The study enrolled 2051 people. At baseline, scabies prevalence was high in all arms (32.1%, 41.7%, 36.6% in the three arms respectively). After one year the prevalence of scabies, previously reported, fell to 1.9% in the ivermectin arm corresponding to a reduction in prevalence of 94%. Scabies prevalence was also reduced to a lesser extent in the two other arms. At two years, scabies prevalence in the ivermectin arm was 3.7%, compared to 13.4% and 15.4% in the other two arms. In conclusion, the effect of MDA, particularly with ivermectin, was long lasting, with very low prevalence maintained even after two years following administration. The study was the first to compare MDA for scabies with the conventional approach of treating symptomatic cases and contacts, and the first to undertake two year follow up. This strategy is likely to be highly beneficial for communities where this disease is endemic.