Salinity stress has been exacerbating continually as a synergistic effect of natural and anthropogenic reasons. Soils are being overburdened with salinity chiefly due to global warming led increased incidences of drought and water evaporation along with multiple human-activities like unsustainable irrigation practices, deforestation, intensive cropping, etc. As a consequence, many important cereal crops like rice, tomato, soyabeans, etc. are facing huge loss in quality and yield owing to compromised osmotic balance. Among several mitigation strategies, Clustered Regularly Interspaced Short Palindromic Repeat-Cas9 (CRISPR/Cas9) system—a popular gene editing tool is gaining popularity to fortify salinity stress tolerance and protect grain yield. CRISPR/Cas9 can be used to knock-down genes responsible for compromising salinity stress tolerance, or in other words, regulate ion transport and activate stress response pathways. Genes like RR22, OsbHLH024, HyPRP1, OsNF-YC5, etc. edited through CRISPR/Cas9 can build salinity resistant crop varieties. Researchers are relying on CRISPR/Cas9 based genome editing to change the plant's DNA without introducing any foreign genetic material, which might ease some regulatory obstacles. However, it also has its own challenges like off-target effects, efficient delivery, risk of unintended consequences, and ethical concerns. Therefore, this chapter will comprehensively address the immense potential of CRISPR-Cas9 system in developing salinity-resistant crops for our agricultural future along with detailed insights on how scientists are addressing multiple challenges associated with CRISPR-Cas9 based salinity stress management.