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Gastrointestinal stromal tumors (GISTs), the most common mesenchymal neoplasms of the digestive tract, are primarily driven by gain-of-function mutations in the receptor tyrosine kinases KIT or PDGFRA. The introduction of imatinib, a selective tyrosine kinase inhibitor (TKI), revolutionized the management of advanced GIST. However, the emergence of drug resistance remains a major clinical challenge, limiting long-term efficacy. Resistance mechanisms are multifactorial, predominantly involving secondary mutations in KIT or PDGFRA that impair TKI binding or stabilize the kinase in an active conformation. Beyond genomic alterations, nonmutational adaptive responses-including dysregulation of noncoding RNAs, metabolic reprogramming, epigenetic modifications, and an immunosuppressive tumor microenvironment-significantly contribute to treatment failure. This review comprehensively analyzes these resistance pathways and discusses the evolution of therapeutic strategies toward precision medicine. Current approaches emphasize molecular subtype-guided first-line therapy, ctDNA-driven sequencing of subsequent lines, and the use of novel TKIs (e.g., avapritinib, ripretinib, bezuclastinib) tailored to specific resistance mutations. Furthermore, we explore emerging modalities such as boron neutron capture therapy (BNCT), which offers a kinase-independent mechanism to target resistant disease, and combination strategies that integrate immunotherapy, epigenetic modulators, and pathway-specific inhibitors. Advances in liquid biopsy and molecular profiling are enabling real-time adaptation of therapy, moving GIST management toward a dynamic, personalized paradigm aimed at overcoming resistance and improving patient outcomes.