The presence of biotic and abiotic reservoirs is a possible indicator of leptospirosis occurrence in Nairobi County, which has a large proportion of informal settlements. Despite these epidemiological risk factors, little or no attention is accorded to leptospirosis. The study assessed the degree of leptospirosis diagnostic capacity in public health facilities within Nairobi County, Kenya. A descriptive cross-sectional study involving 133 clinicians and 15 laboratory personnel across 15 public health facilities was conducted between August and December 2019. The perception of zoonotic management was high as 95% (126) had a strong score while 5% (7) had a weak score. Healthcare facility level (χ2 (3) = 14.09, p < 0.05), professional designation (χ2 (1) = 4.26, p < 0.05) had a significant association with suspecting zoonosis. The length of service as a clinician was a significant predictor of suspecting zoonosis, Wald = 11.11, p < 0.05. Inter-agency collaboration was low as 89% (119) reported a lack of sharing zoonosis information, and only 8% (10) indicated that there was information sharing. The clinical suspicion index was low, 3.8% of the participants suspected the disease in practice, and 2.3% would consider leptospirosis in the differential diagnosis of FUO. All 15 public health facilities lacked leptospirosis laboratory diagnostic capacity. The probable diagnosis of leptospirosis is low due to a low clinical suspicion index and lack of awareness. There is a lack of laboratory diagnostic capacity. Sensitisation of clinicians and laboratory personnel is critical in increasing the diagnostic capacity of leptospirosis.