The Aedes aegypti mosquito is the primary vector of dengue, a neglected disease and a serious public health problem in tropical countries. The control of this vector has been carried out using chemical insecticides, which impact human health. Thus, it is essential to develop natural larvicides that are less harmful to the environment. This study investigates the circadian cycle and larvicidal activity of essential oils from Croton blanchetianus against Aedes aegypti. The leaf oils were extracted by hydrodistillation and analyzed by GC–MS and GC–FID. The circadian study revealed variations in the chemical composition of oils extracted at different times of the day. The main constituents were α-pinene, β-phellandrene, eucalyptol, β-caryophyllene, bicyclogermacrene, and spathulenol. The larvicidal activity showed LC₅₀ values at the following different collection times: 55.294 ± 3.209 μg/mL at 08:00 h; 95.485 ± 2.684 μg/mL at 12:00 h; and 64.883 ± 1.780 μg/mL at 17:00 h. Molecular docking simulations indicated that α-pinene, β-phellandrene, eucalyptol, and β-caryophyllene strongly interact with the active site of the sterol carrier protein, suggesting their role in larvicidal activity. These findings reinforce the potential of C. blanchetianus essential oils as an alternative for Aedes aegypti control. The predictive pharmacokinetic tests showed a PAMPA profile associated with high effective cellular permeability and microsomal stability, resulting from the metabolic stability of the derivatives (3) eucalyptol and (6) spathulenol, indicating that these compounds have the highest pharmacokinetic viability and low reactivity with respect to organ toxicity.