Introduction: Gastrointestinal stromal tumors (GIST), although very rare, are the most common mesenchymal neoplasms of the gastrointestinal tract and develop in approximately 5–25% of patients with neurofibromatosis type 1 (NF1). Neurofibromatosis type 1-associated GIST (NF1-GIST) differ phenotypically and genotypically from sporadic GIST, neither present receptor tyrosine kinase (KIT) or platelet-derived growth factor receptor-alfa (PDGFR-alfa) mutation and have propensity to be multifocal and to occur in the small bowel. Case Report: We present a case of NF1-GIST, with multiple primary lesions, initially diagnosed as metastatic GIST, with treatment implications. Conclusion: Different characteristics of NF1-GIST should be empathized so the evidence of multifocal GIST not be confused with advanced/metastatic GIST, influencing treatment options. Identifying this tumor early allows surgical treatment with potential cure, because GIST are mostly treatable tumors with indolent behavior. Currently, no standard drug therapy for unresectable or relapsed NF1-GIST has been established.