Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. The currently used diagnostic tests are time-consuming, require technical expertise or require the use of sophisticated equipment. Clinicians have pointed out the urgent need to develop a rapid test for the diagnosis of acute leptospirosis with a non-invasive and easy sampling method. In this study, we have focused on a leptospiral enzyme, 3-hydroxyacyl-CoA dehydrogenase (3-HADH), as a urinary biomarker of acute leptospirosis. A specific antiserum for pathogenic Leptospira spp. was produced, targeting a peptide corresponding to amino acids 410 to 424 of 3-HADH. The antiserum was used to investigate whether 3-HADH is excreted in the urine by Western blotting. Among 70 suspected leptospirosis patients, 40 were laboratory confirmed by microscopic agglutination test (MAT) using paired sera samples and/or polymerase chain reaction (PCR). In the acute phase of the laboratory-confirmed leptospirosis cases, sensitivity for 3-HADH, blood PCR and urine PCR were 52.5%, 57.5% and 12%, respectively. 3-HADH was detected from 2 days post-onset of illness (p.o) and could be detected at least until 9 days p.o. The combination of PCR and 3-HADH detection increased sensitivity of diagnosis to 100% in samples collected between 1 and 3 days p.o., and to 82% in samples collected between 4 and 9 days p.o. Our results suggested that the detection of 3-HADH can support a clinical diagnosis of leptospirosis, especially when serological methods are negative during the acute phase.