Pesticide exposure has been associated with various health conditions like asthma, Parkinson’s disease, Alzheimer’s disease, genetic disorders, epigenetic changes, oxidative stress, and hormonal disruption. Recent evidence suggests that infants are more vulnerable to pesticides (such as rotenone) than adults. Although the disease has already been clinically characterized, no treatment has yet been developed to improve pathology or prevent developmental toxicity. Therefore, the purpose of this study was to investigate whether thymoquinone (TQ) from Nigella sativa seeds could ameliorate rotenone (ROT)-induced developmental damage in both Drosophila melanogaster ovary and third instar larvae. Female adult wild-type flies and third instar larvae (72 ± 2 h after egg laying) were exposed to ROT and/or TQ through food for 48 and 24 h respectively. Results indicate that co-exposure of TQ inhibits ROT-induced increased oxidative stress and alleviates abnormal antioxidant enzyme activities. Further, TQ alters developmental gene expression (Bacoid, Oscar, Nanos, and Gurken), impedes mitochondrial dysfunction, and reduces apoptosis in ROT induced ovary. In addition, TQ changes ROT induced abnormal crawling behaviour, cholinergic dysfunction, and dopamine depletion to normal levels in third instar larvae. Also, TQ reduces pupation and emergence time in ROT induced third instar larvae. The above findings demonstrate that ROT exposure during early developmental stages is inevitable, and TQ supplementation prevents developmental toxicity in the Drosophila ovary and third instar larvae. A diet enriched TQ provides a ray of hope in preventing ROT induced developmental toxicity.