Integration of tsetse fly and trypanosomiasis control methods is identified as most feasible and effective approach to eradication of African Animal Trypanosomiasis (AAT) and Human African Trypanosomiasis (HAT). However, little focus is directed towards understanding the drivers of integration of the control methods by farmers. We used cross-sectional data collected from 536 livestock keeping households in Lamu County of Kenya to identify factors influencing multiple use of insecticide treated livestock (ITL), insecticide treated targets (ITT), and treatment with trypanocidal drugs (TTD). Multivariate probit model was applied in estimation of covariates of multiple use of the control methods. Descriptive results indicated that nearly 61% of the livestock keeping households used at least one of the tsetse fly and trypanosomiasis control methods, with about 9%, 7%, and 13% of the households using ITL, ITT, and TTD, respectively. The results also indicated that nearly 32% of the households integrated the control methods. Furthermore, multivariate probit results showed that sex of household head, age of farmer, positive perceptions of technology availability and effectiveness, and off-farm income increased the likelihood of integration. In contrast, household size, having agriculture as the main occupation, and cost of the technology significantly reduced the likelihood of multiple use of the control methods. The results suggest heterogeneity in farmers’ decisions to integrate tsetse fly and trypanosomiasis control methods. Therefore, farmer outreach programs should consider key household characteristics, as well as technological attributes which may stimulate adoption of appropriate tsetse fly and trypanosomiasis control technologies.