This study aimed to compare the clinical relevance of the novel drug rutin trihydrate with doxorubicin concerning their influence on the antioxidant enzymes GST, GPX, and GSH. Zebrafish larvae were subjected to oxidative stress induced by H₂O₂ at 1mM concentration, and their antioxidant activity was assessed through enzymatic assays. The stock solution was prepared with DMSO, and zebrafish eggs were collected in a 1:1 male-to-female breeding ratio, followed by distribution into four petri plates for exposure to rutin trihydrate from 4 hours post-fertilization (hpf) to 96 hpf. Hatching rates were recorded after 96 hpf, and SPSS software was utilized for statistical analysis. Embryos exposed to compound dosage exhibited significantly increased enzyme activity (p < 0.000, p < 0.05) (8.5667.17593) compared to appropriate dosages (34.40000.07). With a total sample size of 30 and parameters including a 0.05 significance threshold, 80% statistical power, a 95% confidence interval, and an enrolment ratio of 1, the study revealed notable alterations in GPX (9%), GSH (5%), and GST (5%) activity in zebrafish larvae treated with rutin trihydrate and doxorubicin. The investigation’s significance level was determined to be p = 0.000 (p < 0.05), signifying a statistically significant difference among the test groups. These findings shed light on the potential clinical implications of these compounds on zebrafish larvae’s antioxidant systems.