In May 2025, Mombasa County reported an increase in cases of acute febrile illness with severe joint pain, prompting suspicion of a Chikungunya virus outbreak. Initial laboratory testing confirmed 21 out of 36 samples (58%) positive for Chikungunya virus by RT-PCR, with one additional case testing positive for Dengue virus. Following the official outbreak declaration on June 9, 2025, the Mombasa County Department of Health requested that the Kenya National Public Health Institute (KNPHI) support the investigation into the outbreak and provide recommendations.

A multidisciplinary team from the Kenya National Public Health Institute (KNPHI) and the Field Epidemiology and Laboratory Training Program (FELTP) was deployed between June 12th and 19th, 2025, to investigate the magnitude of the outbreak, characterize the cases, determine the factors associated with outbreak, and strengthen prevention and control measures for Chikungunya in the county. The team conducted retrospective record reviews from March 2025 to June 2025, active case finding, household surveys, environmental assessments, and laboratory testing.

The findings confirmed active Chikungunya transmission in the county, driven by vector-friendly environmental conditions and limited public awareness. Immediate and long-term recommendations include enhanced surveillance, targeted vector control, improved diagnostic capacity, and ongoing community education to prevent future outbreaks.