As important secondary plant metabolites, naphthoquinones exhibit a wide range of biological activities. However, their potential as sustainable alternatives to synthetic acaricides has not been studied. This study for the first time investigates the acaricidal activity of naphthoquinones against Psoroptes cuniculi in vitro. Furthermore, the in vivo activity, the skin irritation effects, the cytotoxicity and the inhibitory activities against mite acetylcholinesterase (AChE) and glutathione S-transferase (GST) of the two compounds that displayed the best insecticidal activity in vitro were evaluated. Among fourteen naphthoquinones and their analogs, juglone and plumbagin were observed to possess the strongest acaricidal activities against P. cuniculi with LC50 values of 20.53 ppm and 17.96 ppm, respectively, at 24 h. After three treatments, these two chemicals completely cured naturally infested rabbits in vivo within 15 days, and no skin irritation was found in any of the treated rabbits. Compared to plumbagin, juglone presented no or weak cytotoxicity against HL-7702 cells. Moreover, these two chemicals significantly inhibited AChE and GST activity. These results indicate that juglone has promising toxicity against P. cuniculi, is safe for both humans and animals at certain doses, and could be used as a potential alternative bio-acaricide for controlling the development of psoroptic mange in agricultural applications.