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Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired hemolytic disorder, caused by impaired cell surface expression of GPI-anchors in hematopoietic cells as a result of somatic mutation in the PIG-A gene, and often progresses into bone marrow aplasia. We experienced a girl diagnosed as having PNH with spontaneous recovery from pancytopenia, and analyzed the GPI-anchor expression on peripheral blood cells. Thrombocytopenia was first determined when she was 5-years old, and Ham and sugar water tests were negative at the age of 6 years. Subsequently, the pancytopenia slowly progressed, and the diagnosis of PNH was made at the age of 8 years based on the positive Ham test. Frame-shift of the PIG-A gene in exon 2 was confirmed in the peripheral granulocytes at the age of 11 years. Pancytopenia spontaneously subsided over two years after diagnosis, and an almost normal hematogram except for mild thrombocytopenia has been maintained for the subsequent 4 years. In periodical flow cytometric analysis of the CD55 expression on granulocytes and erythrocytes and the CD48 expression on lymphocytes, the population of the PNH clone was almost unchanged during the first two years of spontaneous recovery, but that of CD55-negative erythrocytes gradually decreased, suggesting that regression of PNH clone might be unnecessary in transient improvement of pancytopenia.