Pernicious anemia is an autoimmune disease leading to impaired absorption of dietary cobalamin. Patients with pernicious anemia can present with multiple hematological, neurological and gastrointestinal complaints. Herein, we have a case of pernicious anemia presenting with alternating bowel habit. This was challenging and unique as the patient didn't have any usual condition responsible for alternating bowel habit and it is not reported in cases of pernicious anemia either. The case is a 46-year-old male who was admitted with alternating bowel habit, paresthesia and fever for the last 6 months. Patient was found to be severely anemic. After full workup, he was diagnosed with pernicious anemia. The patient was treated with IM Injections of Vitamin B12. After 3 months of discharge, the patient was free of all the symptoms. This case emphasizes the importance of investigating anemic patients with alternating bowel habit for pernicious anemia and also the need to exclude other causes of this symptom before labeling it as pernicious anemia only.