Context Vector-borne diseases have caused global pandemics and were responsible for more human deaths than all other causes combined in prior centuries. In the past 60 years, prevention and control programs have helped reduce human mortality from vector-borne diseases, but impacts of those control programs on wildlife populations are not well documented. Insecticides are used to reduce vector-borne diseases in several critically endangered animal populations. Although insecticides are often effective at controlling targeted vectors, their effects on non-target species have rarely been examined. Aims To evaluate the impact of deltamethrin (an insecticide) on sympatric non-target species in areas affected by sylvatic plague, a lethal flea-borne zoonosis. Methods We compared flea control and the effect of deltamethrin application on survival of non-target small mammals (Peromyscus maniculatus, Chaetodipus hispidus, Microtus spp., and Reithrodontomys megalotis) at three study locations in South Dakota, Colorado, and Idaho, USA. Key results Deltamethrin treatments were more effective in reducing fleas on P. maniculatus and Microtus spp. than C. hispidus. Following burrow, nest, and bait-station applications of deltamethrin dust, apparent small mammal survival was greater for non-treatment animals than for flea-reduction animals. However, the magnitude of the difference between treated and non-treated animals differed among host species, study location, time interval, and treatment application method. Conclusions Our results suggest that considering the impact of deltamethrin on co-occurring non-target species before widespread application in future insecticide applications is warranted. Implications Insecticide application methods warrant consideration when designing plague management actions.