A retrospective study was conducted in 2022 to determine the seroprevalence of brucellosis and its risk factors among goat and sheep herds in the Karenga district, Karamoja region, Uganda. Sera from 332 goats and 81 sheep from 20 kraals in all seven administrative units of the district were tested using the modified Rose Bengal test (mRBT). It was determined that brucellosis was present in 20% of the small ruminant herds in the Karenga district, with an overall animal level seropositivity of 3.39% (CI: 1.87–5.62%; n = 14/413). Higher seropositivity was recorded in goats (3.92%, CI: 2.1–6.6%) than sheep (1.23%, CI: 0.03–6.69%). Similarly, seropositivity was higher in females (3.95%, CI: 2.12–6.66%) than males (1.19%, CI: 0.03–6.456), and also higher in goats and sheep more than two years old (4.15%, CI: 2.09–7.31%) than those one to two years old (1.98%, CI: 0.24–6.97%) or those less than one year old (2.13%, CI: 0.05–11.29%). Only herd size was statistically significant (p < 0.05) as a risk factor for exposure to brucellosis in the Karenga district. Although the prevalence of brucellosis among goats and sheep in the Karenga district is low, there still exists a risk to the pastoralists who closely interact with the animals and also practice risky behaviours such as consumption of uncooked or unpasteurised goat milk. There is need to expand herd health messaging in Karenga to include risk communication on brucellosis and other zoonotic diseases.