Small RNA sequencing was performed to profile microRNA expression in mouse kidneys after transplantation. Lentivirus incorporating a miR-199a-5p modulator was injected into mouse kidney in situ before unilateral IRI and syngenetic transplantation, to determine the effect of miR-199a-5p in vivo. miR-199a-5p mimic or inhibitor was transfected cultured tubular cells before renal tubular ATP depletion recovery treatment to the examine the role of miR-199a-5p in vitro. Sequencing showed upregulation of miR-199a-5p in post-transplantation mouse kidney following renal IRI was localized to renal tubular epithelial cells. Lentivirus incorporating a miR-199a-5p mimic aggravated renal IRI and opposing effects were obtained with a miR-199a-5p inhibitor. Treatment with the miR-199a-5p inhibitor ameliorated graft function loss, tubular injury and immune response after cold storage transplantation. In vitro experiments demonstrated aggravation of cell death caused by ATP depletion and repletion when the miR-199a-5p mimic was present while the miR-199a-5p inhibitor reduced cell death. miR-199a-5p was shown to target a-kinase anchoring protein 1(AKAP1) by double luciferase assay and miR-199a-5p activation reduced dynamin related protein 1 (Drp1)-s637 phosphorylation and mitochondrial length. Overexpression of AKAP1 preserved Drp1-s637 phosphorylation and reduced mitochondrial fission. MiR-199a-5p activation reduced AKAP1 expression, promoted Drp1-s637 dephosphorylation, aggravated the disruption of mitochondrial dynamics and contributed to ischemic kidney injury.