Gene therapy offers transformative potential for treating genetic disorders by directly addressing the molecular root causes of diseases. However, the primary challenges of gene therapy involve the efficient delivery of therapeutic genetic material to target cells, crossing biological barriers, managing toxicity and immune responses. Mesoporous silica nanoparticles (MSNs), due to their unique structural features have emerged as a promising platform to overcome these challenges. In recent years, MSNs have gained significant attention as potential nanocarriers for the efficient delivery of various nucleic acids. This review comprehensively examines the role of MSNs in gene therapy, focusing on their capabilities in the targeted delivery of siRNA, DNA, CRISPR-Cas systems, and other genetic therapeutics. This work explores the modern advancements in MSNs synthesis and functionalization strategies and the impact of structural modifications on their stability, cellular uptake, and controlled release under physiological conditions. Additionally, the review highlights the use of MSNs to develop theranostic systems, where gene delivery is combined with diagnostic imaging for real-time monitoring and personalized treatment strategies. Finally, this work discusses the future perspectives of MSNs in gene delivery, addressing regulatory challenges, enhancing clinical translation, and expanding their application for treating various genetic disorders and cancers.