No to less effort has been made to assess the toxicity of silver nanoparticles (AgNPs) to lipid composition in biological systems and also to discover a mitigating agent against their oxidative stress. Hence, this research evaluated the antioxidant capability of quercetin (Qu) against silver nanoparticles (AgNPs) toxicity towards the lipid contents of ovarian, nervous, and hepatic systems as well as skeletal muscles. To this end, zebrafish (n = 180) were assigned into four experimental dietary groups: negative and positive controls, without Qu supplementation; Qu-200, 200 mg Qu per kg diet; and Qu-400, 400 mg Qu per kg diet. At the end of the feeding trial (40 days), the experimental groups, except the negative control, were exposed to sublethal concentration of AgNPs (0.15 mg L−1) for 96 h. As to the liver tissue of the positive and Qu-200 treatments, total polyunsaturated fatty acids (∑PUFA) decreased 3 times, as well as total high unsaturated fatty acids (∑HUFA) reduced about 30% and 50%, respectively. However, the brain ∑HUFA, predominated by DHA, enhanced in Qu-400 treatment. Interestingly, ∑MUFA, ∑PUFA, and ∑HUFA increased in the muscle of all treated groups, especially Qu-200 and Qu-400. The oocyte ∑MUFA content increased in the positive and Qu-200 treatments, whereas ∑HUFA reduced about 25%, 25%, and 20%, respectively, in the positive, Qu-200, and Qu-400 groups. Generally, the findings suggest that unsaturated acyl chains, particularly HUFAs, in the liver tissue and oocyte cell are highly susceptible to peroxidation or degeneration by AgNPs. More broadly, in the context of ecotoxicological risk assessment, the alteration in HUFAs and PUFAs of the liver and oocyte could impact on maternal and offspring health and consequently alter long-term population dynamics of aquatic animals.