Paroxysmal nocturnal haemoglobinuria (PNH) is a rare disease characterized by intravascular haemolysis, haemoglobinuria and thrombosis. The present study reported PNH patients presenting with isolated thrombocytopenia. A 31-year-old male patient was referred to haematology outpatient clinic because of thrombocytopenia detection. Initially, there was no anaemia, but apparent haemolytic anaemia occurred in the patient within a year. The PNH was diagnosed by using fluorescently labelled inactive variant of the protein aerolysin test. Anaemia, jaundice, thrombosis, fatigue, dyspnoea, dark urine, abdominal or gastric pain, dysphagia and erectile dysfunction are primary symptoms of PNH, leading to diagnosis. This is an atypical PNH case presenting with isolated thrombocytopenia, which led to difficulty and delay in diagnosis.