Systemic mastocytosis (SM) is a malignant hematopoietic disorder characterized by the clonal proliferation and accumulation of aberrant mast cells in one or more extracutaneous organs such as the gastrointestinal tract, bone marrow, spleen, and liver. Diarrhea is one of the most common symptoms of SM, affecting more than 70% of patients. However, diarrhea is a general gastrointestinal symptom that can be attributed to many common causes, including diarrhea-predominant irritable bowel syndrome (IBS-D). This can delay the diagnosis of SM-related diarrhea, specifically in patients who do not have other typical SM symptoms, such as skin manifestations or anaphylaxis. Given its rarity, SM can be difficult to diagnose due to its diverse clinical manifestations and general practitioners’ lack of awareness. Additionally, SM can evade detection through standard endoscopy and colonoscopy procedures if there is no clinical suspicion. However, several tests can be used to diagnose SM, including endoscopic biopsy, KIT D816V mutation testing, bone marrow biopsy, and serum tryptase levels. Treatment of SM is tailored to the individual patient’s disease characteristics and symptoms. Symptomatic treatment to control mast cell mediator-related features and cytoreductive therapy are the mainstays of SM management. This review sheds light on the main aspects of gastrointestinal involvement by systemic mastocytosis, as highlighted by a case report of a patient initially diagnosed with refractory IBS-D. This review aims to increase awareness of the clinical diversity of SM.