The promise of viral vector‐based gene therapy (GT) as a transformative paradigm for treating severely debilitating and life‐threatening diseases is slowly coming to fruition with the recent approval of several drug products. However, they have a unique mechanism of action often necessitating a tortuous clinical development plan. Expertise in such complex therapeutic modality is still fairly limited in this emerging class of adeno‐associated virus (AAV) vector‐based gene therapies. Because of the irreversible mode of action and incomplete understanding of genotype–phenotype relationship and disease progression in rare diseases careful considerations should be given to GT product's benefit–risk profile. In particular, special attention needs to be paid to safe dose selection, reliable dose exposure response (including clinically relevant endpoints), or creative approaches in study design targeting small patient populations during clinical development. We believe that quantitative tools encompassed within model‐informed drug development (MIDD) framework fits quite well in the development of such novel therapies, as they enable us to benefit from the totality of data approach in order to support dose selection as well as optimize clinical trial designs, end point selection, and patient enrichment. In this thought leadership paper, we provide our collective experiences, identify challenges, and suggest areas of improvement in applications of modeling and innovative trial design in development of AAV‐based GT products and reflect on the challenges and opportunities for incorporating MIDD tools and more in rational development of these products.