Small ruminant production is a key component of pastoral livelihoods and food security in Mandera County, Kenya. This study investigated disease occurrence, veterinary delivery, climate impacts, market integration, and value chain constraints affecting Mandera County's small ruminant industry to fill a gap in integrated evidence. Using a mixed-methods cross-sectional design, researchers combined structured surveys of 370 pastoralist households across six sub-counties, six focus group discussions, six key informant interviews with veterinary and extension officers, and a review of 2022–2024 climate records. Regression analysis, Pearson correlation, one-way ANOVA and thematic analysis were applied. Reported disease occurrence was high, with 68.1% of respondents reporting PPR in goat herds and 71.9% in sheep flocks, while 41.9% reported CCPP occurrence in goats. Veterinary service access was limited, with only 31.9% of pastoralists reporting regular access, due to geographical barriers (60.8% living beyond 15 km) and financial constraints (81.9% reporting services as unaffordable). Climate variability impacts were substantial, with 89.0% of respondents reporting changes, particularly increased drought frequency (67.0%) and unpredictable rainfall (45.0%), leading to reduced herd sizes (72.0%) and high mortality (40.0%). Market integration was constrained by dominant local market channels (65.1%), information asymmetries and limited value addition (72.0%). Regression analysis accounted for 79.4% of the variation in small ruminant industry performance (R² = 0.794, Adjusted R² = 0.780, p < 0.001), identifying drought frequency (β = -0.387, p < 0.001), reported PPR occurrence (β = -0.245, p < 0.001) and market access (β = 0.275, p < 0.001) as the strongest predictors. Disease burden, inadequate veterinary services, climate stress and market integration constraints are significantly associated with reduced industry performance in Mandera County. The study recommends establishing community-based animal health worker systems, implementing climate-resilient feeding strategies and developing pastoralist cooperatives for improved market integration.