BackgroundAs a core member of the FA complex, in the Fanconi anemia pathway,FAAP24plays an important role in DNA damage repair. However, the association betweenFAAP24and patient prognosis in AML and immune infiltration remains unclear. The purpose of this study was to explore its expression characteristics, immune infiltration pattern, prognostic value and biological function using TCGA-AML and to verify it in the Beat AML cohort.MethodsIn this study, we examined the expression and prognostic value ofFAAP24across cancers using data from TCGA, TARGET, GTEx, and GEPIA2. To further investigate the prognosis in AML, development and validation of a nomogram containingFAAP24were performed. GO/KEGG, ssGSEA, GSVA and xCell were utilized to explore the functional enrichment and immunological features ofFAAP24in AML. Drug sensitivity analysis used data from the CellMiner website, and the results were confirmed in vitro.ResultsIntegrated analysis of the TCGA, TARGET and GTEx databases showed thatFAAP24is upregulated in AML; meanwhile, highFAAP24expression was associated with poor prognosis according to GEPIA2. Gene set enrichment analysis revealed thatFAAP24is implicated in pathways involved in DNA damage repair, the cell cycle and cancer. Components of the immune microenvironment using xCell indicate thatFAAP24shapes an immunosuppressive tumor microenvironment (TME) in AML, which helps to promote AML progression. Drug sensitivity analysis showed a significant correlation between highFAAP24expression and chelerythrine resistance. In conclusion,FAAP24could serve as a novel prognostic biomarker and play an immunomodulatory role in AML.ConclusionsIn summary,FAAP24is a promising prognostic biomarker in AML that requires further exploration and confirmation.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12935-023-02937-3.