Background/Objectives: Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by motor and cognitive impairments due to dopaminergic neuron loss. The neurotoxin MPTP is commonly used to model PD, as it selectively targets these neurons. Quercetin (QU), a flavonoid with antioxidant properties, has shown neuroprotective potential, but its poor solubility limits clinical application. Nanoemulsions (NEQU) have emerged as a strategy to enhance its bioavailability and efficacy. Methods: To evaluate the neuroprotective and antioxidant effects of QU and NEQU, zebrafish larvae were exposed to MPTP (50 µM) and assessed for survival, locomotion (total distance traveled), morphological parameters, reactive oxygen species (ROS), lipid peroxidation (via MDA), and reduced glutathione (GSH) levels. Results: Only NEQU pre-treatment reversed MPTP-induced locomotor deficits. Both QU and NEQU (2.5 µM) significantly reduced ROS production and lipid peroxidation, with no effect on GSH levels. Notably, MPTP exposure led to a significant reduction in head size, an unprecedented finding in zebrafish PD models, indicating neurotoxicity. Morphometric analysis showed no change in total body length. However, MPTP significantly decreased swim bladder size and increased yolk sac size. Treatment with QU and NEQU attenuated these swim bladder alterations; no significant differences were observed in other parameters. Conclusions: These findings suggest that quercetin, particularly when nanoencapsulated, is a promising candidate for further development as a therapeutic agent to mitigate PD-related neurodegeneration.