Tick infestation is a serious problem in many countries since it has an impact on the health of animals used for food production and pets, and frequently affects humans. Therefore, the present study aimed to investigate the acaricidal effects of nanoemulsions of essential oils of Melaleuca alternifolia (tea tree, TT) and Citrus limon (lemon oil, CL) against the different stages (adult, eggs, and larvae) of deltamethrin-resistant Rhipicephalus annulatus ticks. Three forms of these oils were tested: pure oils, nanoemulsions, and a binary combination. Tea tree and lemon oil nanoemulsions were prepared, and their properties were assessed using a zeta droplet size measurement and a UV-Vis spectrophotometer. The results showed that TT and CL exhibited higher adulticidal effects in their pure forms than in their nanoemulsion forms, as demonstrated by the lower concentrations required to achieve LC50 (2.05 and 1.26%, vs. 12.8 and 11.4%, respectively) and LC90 (4.01% and 2.62%, vs. 20.8 and 19.9%, respectively). Significant larvicidal activity was induced by the TTCL combination, and LC50 was reached at a lower concentration (0.79%) than that required for the pure and nanoemulsion forms. The use of pure CL oil was found to have the most effective ovicidal effects. In conclusion, pure TT and CL have potent acaricidal effects against phenotypically resistant R. annulatus isolates. It is interesting that the activity levels of TT and CL EOs’ binary and nanoemulsion forms were lower than those of their individual pure forms.