Thrombopoietin (THPO) is a regulator of megakaryopoiesis and thrombopoiesis. Mutation of the THPO gene is known to cause congenital amegakaryocytic thrombocytopenia (CAMT2), which is a rare inherited disorder characterized by early infancy thrombocytopenia and absent or decreased megakaryocytes with gradual progression to pancytopenia. We report the case of a Saudi girl who had been asymptomatic until age seven when she was found to have unexplained thrombocytopenia. Whole-genome sequencing detected loss between the genomic coordinates (chr3:184088108-184090520) partially encompassing exon 6 of the THPO gene in a homozygous state, which is reported as a new variant. This report highlights the importance of genetic testing for unexplained persistent hematological abnormalities for early diagnosis, especially in consanguineous populations.