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The active form of vitamin D₃, i.e., 1,25(OH)₂D₃, exerts an anti-inflammatory effect on the immune system, especially macrophage-mediated innate immunity. In a previous study, we identified 1,25(OH)₂D₃-responsive and vitamin D receptor (VDR)-bound super-enhancer regions in THP-1 cells. Herein, we examined the transcriptional regulation of <i>ArfGAP with SH3 Domain, Ankyrin Repeat and PH Domain 2</i> (<i>ASAP2</i>) (encoding a GTPase-activating protein) by 1,25(OH)₂D₃ through the top-ranked VDR-bound super-enhancer region in the first intron of <i>ASAP2</i> and potential functions of ASAP2 in macrophages. First, we validated the upregulation of <i>ASAP2</i> by 1,25(OH)₂D₃ in both THP-1 cells and macrophages. Subsequently, we identified three regulatory regions (i.e., the core, 1,25(OH)₂D₃-responsive, and inhibitory regions) in the VDR bound-enhancer of <i>ASAP2</i>. ASAP2 promoted RAC1-activity and macrophage efferocytosis in vitro. Next, we assessed the functions of ASAP2 by mass spectrometry and RNA sequencing analyses. ASAP2 upregulated the expressions of antiviral-associated genes and interacted with SAM and HD domain-containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1). In vivo, vitamin D reduced the number of apoptotic cells in experimental autoimmune encephalomyelitis (EAE) and promoted macrophage efferocytosis in peritonitis without changing the mRNA level of <i>ASAP2</i>. Thus, we could better understand the regulatory mechanism underlying <i>ASAP2</i> transcription and the function of ASAP2, which may serve as a potential treatment target against inflammatory diseases and virus infections.