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Renal leptospirosis caused by leptospiral infection is characterised by tubulointerstitial nephritis and tubular dysfunction, resulting in acute and chronic kidney injury. Metabolomic and transcriptomic data from a murine model of <i>Leptospira</i> infection were analysed to determine whether metabolomic data from urine were associated with transcriptome changes relevant to kidney injury caused by <i>Leptospira</i> infection. Our findings revealed that 37 metabolites from the urine of <i>L. interrogans</i>-infected mice had significantly different concentrations than <i>L. biflexa</i>-infected and non-infected control mice. Of these, urinary L-carnitine and acetyl-L-carnitine levels were remarkably elevated in <i>L. interrogans</i>-infected mice. Using an integrated pathway analysis, we found that L-carnitine and acetyl-L-carnitine were involved in metabolic pathways such as fatty acid activation, the mitochondrial L-carnitine shuttle pathway, and triacylglycerol biosynthesis that were enriched in the renal tissues of the <i>L. interrogans</i>-infected mice. This study highlights that L-carnitine and acetyl-L-carnitine are implicated in leptospiral infection-induced kidney injury, suggesting their potential as metabolic modulators.