FA is a rare, multi-organ cancer-prone IBMFS associated with hematological malignancies and STs. The androgen therapy, hematopoietic growth factors, HSCT, and GT, still in the clinical trial, are various treatments for this disease. Here, we aimed to compare the advantages and disadvantages of HSCT and GT in FA cures. We perform an advanced electronic search of “FA” AND (genetics OR treatment OR HSCT OR GT OR Mosaicism), and “Allo-HSCT” AND (conditioning regimen OR complications OR GvHD OR infection OR cost) MeSH terms in non-citation and citation databases. Besides, the gray literature was searched too. This article will provide a summary of the advantages and disadvantages of HSCT and GT of FA disease. Our results show that GT has a good potential in FA treatments in the future. Furthermore, it has higher advantages and fewer disadvantages in comparison with HSCT. Systematic Review Registration: CRD42021247364 ID on PROSPERO database.