Background: Mast cell leukemia (MCL) is a highly life-threatening and extremely rare subtype of systemic mastocytosis (SM). MCL, divided into de novo subtype and secondary to mastocytosis subtype, often genetically contains one or more somatic mutations, particularly the activating mutations of KIT. In this study, an acute MCL case was reported, who had rare phenotype and genetic mutants with a history of primary malignant mediastinal germ cell tumor (GCT).Case presentation: A male patient aged 30, who underwent two rounds of surgery and chemotherapy with a history of malignant mediastinal GCT, was admitted to our hospital due to persistent chest pain and severe fatigue. The diagnosis of acute MCL was confirmed by morphology analysis and chemical staining of marrow aspirate and biopsy, with the addition of C-findings including splenomegaly and cytopenia. The atypical MCs phenotypically expressed CD9, but no CD2 and CD25. Next gene sequencing of marrow aspirate identified heterozygous mutations in TP53 P301Qfs*44, FLT3 R973X, SETBP1 N272D, and JAK3 I688F, whereas the mutations in KIT were not found. Although the initial therapy of corticosteroids and dasatinib-based regimen was effective, he died of acute respiratory distress syndrome after the first cycle of chemotherapy with cladribine and cytarabine. The survival time of the patient was 2.4 months after the initial presentation of MCL. Conclusion: In this case, MCL preceded by malignant mediastinal GCT has similar clinical symptoms and morphological manifestations but distinctly different genetic profiles in contrast to primary MCL. The characteristic morphology of MCL provides the most pivotal evidence that led our diagnosis in the right direction. A hypothesis was speculated that there is a common embryonal cancer stem cell between primary malignant GCT and secondary de novo MCL, whereas the latter is gradually developed in the context of additional “driver mutations”.