This study examined the larvicidal effect of trunk-injected abamectin and emamectin benzoate against the walnut husk fly (Rhagoletis completa Cresson, 1929). Walnut trees in two locations in two years were injected with the pesticides at different concentrations. For the toxicokinetic studies, the active ingredient content was measured in the leaves, flowers, husks, and kernels, using a UHPLC-MS/MS analytical method. The walnut husk fly infestation rates were between 3 and 70% and 10 and 34% for abamectin and emamectin benzoate, respectively, and were much lower compared to those measured for the control. The active ingredient content in the walnut husk showed a positive correlation with the larvicidal effect. The injections had a measurable but unsatisfactory insecticidal effect in the second year, when the economic threshold was exceeded. Trace amounts of the active ingredients were detected in the flowers. The residue analysis showed a declining concentration trend in the leaves over time. The largest quantities were detected in the leaves (≤439 ng/g of abamectin; ≤19,079 ng/g of emamectin benzoate), with concentrations in the husks of orders of magnitude lower (≤5.86 ng/g; ≤50.19 ng/g). The measurements showed no active ingredient residue above the MRLs in either fresh or dried kernels. The results indicate that trunk injections of abamectin, as well as trunk injections of emamectin benzoate, have the potential to suppress walnut husk fly populations.