Background: Ayurveda prioritises individualised healthcare through Prakriti (constitutional phenotype) assessment and rejuvenation through Rasayana therapy. The emerging discipline of Ayurgenomics aims to correlate these traditional concepts with molecular and genomic frameworks. Despite this, there is a scarcity of experimentally tractable models for validating these principles. Zebrafish (Danio rerio) have become prominent in translational research because of their genetic similarity to humans, optical transparency, rapid development, and compatibility with high-throughput and multi-omics methodologies. Materials and Methods: The scoping review was conducted in accordance with the Arksey and O’Malley framework and PRISMA-ScR guidelines. Electronic searches of PubMed, Scopus, Web of Science, MEDLINE, ScienceDirect, and Google Scholar were conducted for literature published up to December 2025 using terms related to zebrafish/Danio rerio, Ayurveda, Rasayana, Ayurgenomics, and traditional herbal medicines. Two reviewers independently screened titles/abstracts and full texts using predefined eligibility criteria. Of 1,245 records identified, 150 studies met the inclusion criteria. Results: The evidence indicates that zebrafish effectively model developmental toxicity, organ-specific and molecular responses, modulation of oxidative stress, neurobehavioral alterations, metabolic regulation, and tissue regeneration. High-throughput embryo assays and disease-specific models facilitate mechanistic validation of herbal interventions. Nevertheless, the integration of Prakriti-based stratification and constitution-specific frameworks is limited, as most studies focus on isolated compounds rather than polyherbal or personalised approaches. Conclusion: Zebrafish constitute a robust yet underutilised translational platform for advancing evidence-based Rasayana research and Ayurgenomics. The integration of multi-omics tools, standardised protocols, and constitution-oriented experimental designs has the potential to enhance precision-based Ayurvedic therapeutics and facilitate the integration of traditional knowledge with contemporary biomedical science.