Background and purpose MicroRNAs (miRNAs) have been demonstrated to play crucial roles in the early stage of acute ischaemic stroke (AIS). The purpose of this study was to investigate the expression patterns of miRNAs in peripheral blood mononuclear cells (PBMCs) from AIS patients and further explore related molecular mechanisms in stroke‐induced immunodeficiency syndrome (SIDS). Methods The miRNA expression patterns of PBMCs were detected by miRNA microarray and validated by quantitative real‐time polymerase chain reaction (qRT‐PCR) in AIS patients and healthy controls. Bioinformatics methods and luciferase reporter assays were used to detect the downstream target genes. Following stimulation with lipopolysaccharide and interleukin‐4, the expression of miR‐4443, tumor necrosis factor receptor associated factor 4 (TRAF4) and the nuclear factor kappa B (NF‐κB) pathway were evaluated. Furthermore, transfection with miR‐4443 mimic or inhibitor in the monocytes was carried out to gain insight into the mechanisms in SIDS. Results Interleukin‐10 in AIS patients was significantly higher than that of healthy controls. The miRNA microarray analysis and qRTPCR validation showed that only miR‐4443 was upregulated expressed in PBMCs from AIS patients, especially in monocytes. miR‐4443 was shown to directly interact with the 3′ untranslated regions of TRAF4, resulting in suppression of TRAF4 protein expression. Furthermore, the expression of miR‐4443 and TRAF4 was regulated by stimulation with lipopolysaccharide or interleukin‐4. Additionally, overexpression of miR‐4443 suppressed the TRAF4/Iκα/NF‐κB signaling pathway to activate the expression of anti‐inflammatory cytokines in monocytes. Conclusions The increased expression of miR‐4443 induced monocyte dysfunction by targeting TRAF4, which may function as a crucial mediator in SIDS.