Background: Malaria, a disease caused by protozoan parasites of the genus Plasmodium and transmitted by female anopheline mosquitoes, is a major cause of morbidity, mortality and loss in productivity in humans. Baringo County is prone to seasonal transmissions of malaria mostly in the rainy seasons. Methods: This cross-sectional study used a mixed methods approach to collect data on knowledge and lay management of malaria. A questionnaire survey was administered to 560 respondents while qualitative data was collected through 20 focus group discussions in four ecological zones covering Baringo North, Baringo South and Marigat sub-Counties of Baringo County. Analyses were done through summary and inferential statistics for quantitative data and content analysis for qualitative data. Results: The study communities were knowledgeable of malaria signs, symptoms, cause and seasonality but this biomedical knowledge co-existed with other local perceptions. This knowledge, however, did not influence their first (p = 0.77) or second choice treatments (p = 0.49) and compliance to medication (p = 0.84). Up to 88 % of respondents reported having suffered from malaria. At the onset of a suspected malaria case community members reported the following: 28.9 % visited a health facility, 37.2 % used analgesics, 26.6 % herbal treatments, 2.2 % remnant malaria medicines, 2.2 % over the counter malaria medicines, 1 % traditional healers and 1.8 % other treatments. Nearly all respondents (97.8 %) reported visiting a health facility for subsequent treatments. Herbal treatments comprised of infusions and decoctions derived from roots, barks and leaves of plants believed to have medicinal value. Compliance to conventional malaria treatment regime was, however, identified as a challenge in malaria management. Quick relief from symptoms, undesirable qualities like drug bitterness and bad smell, undesirable side-effects, such as nausea and long regimen of treatment were some of the contributors to non-compliance. Men and women exhibited different health-seeking behaviours based on the cultural expectations of masculinity, femininity, gender roles and acceptability of health services. Conclusions: While knowledge of malaria is important in identifying the disease, it does not necessarily lead to good management practice. Treatment-seeking behaviour is also influenced by perceived cause, severity of disease, timing, anticipated cost of seeking treatment and gender, besides the availability of both traditional and conventional medicines.