Isolated thrombocytopenia in adults is a common clinical problem, often caused by various hematological disorders. However, vitamin B12 deficiency as a rare cause of isolated thrombocytopenia has been rarely reported in the medical literature. This case report aims to highlight the diagnostic challenges associated with atypical presentations of thrombocytopenia and emphasizes the importance of considering nutritional deficiencies, such as vitamin B12 deficiency, in the diagnostic workup. We report the case of a 38-year-old male who presented with generalized weakness, fatigue, and a history of bruises without trauma. Physical examination and laboratory investigations revealed thrombocytopenia (42 K/µL) with normal red blood cell morphology and no apparent abnormalities in other hematological parameters. Serum vitamin B12 levels were significantly diminished (128 pg/ml). The patient was treated with subcutaneous mecobalamin 1000 mcg supplementation, resulting in improvements in serum vitamin B12 levels (772 pg/ml) and platelet count (154 × 109/L) values. This case highlights the importance of considering vitamin B12 deficiency as a potential cause of isolated thrombocytopenia in adults. The lack of hypersegmented neutrophils and characteristic signs of macrocytic anemia in the context of vitamin B12 deficiency emphasizes the necessity for a thorough investigation to rule out other possible causes. Hematological problems associated with thrombocytopenia caused by vitamin B12 deficiency can be treated early to resolve them and avoid complications.