The zinc oxide nanoparticles (ZnO-NPs) being widely employed in several industries and consumer products, are raising concerns about their safety on aquatic biota and human health. This study aims to investigate the possible toxicological effects of ZnO-NPs through a combined in vivo and in silico approach. Zebrafish embryos were exposed to several ZnO-NPs concentrations and morphological alterations and lipid peroxidation (MDA) were investigated. Furthermore, molecular docking simulations were applied to study the intermolecular interactions of ZnO-NPs against critical embryonic proteins namely zebrafish hatching enzyme1 (ZHE1) as well as the superoxide dismutase (SOD1). Treatment with ZnO-NPs resulted in an increase in MDA concentration and a decrease in antioxidant enzyme levels. Besides a significant decrease in mRNA expression of key enzymes of ROS detoxification genes, a modulation of inflammatory genes with a low downregulation of tnf-α, and an upregulation of il-1β were observed. Docking study suggests that the delayed hatching and increased cellular oxidative stress in zebrafish embryos may occur through a synergistic mechanism based on the ZnO-NP—dependent inhibition of ZHE1 and SOD1 enzymes. The integration of in vivo assessments with in silico computational modeling provided a more comprehensive evaluation of potential physiological risks in zebrafish embryos associated with nanomaterial exposure.