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This cross-sectional study aimed to study animal, farm, and within-farm seroprevalence of C. burnetii and to identify associated risk factors in goat and sheep farm in northern Jordan. Questionnaire was developed to collect information about risk factors and farms management practices. Blood samples from 730, ≥ 1-year-old females (goat n = 250; sheep n = 480) were randomly collected from 20 goat herds and 40 sheep flocks. IDEXX ELISA Kit was used to detect C. burnetii antibodies. The overall goat and sheep seroprevalence level was 32.5% (237/730) and was significantly higher in goats (43.3%, 108/250; 95% CI 37-49.6) than sheep (27%, 129/480; 95% CI 29.1-36.2) (χ2 test, p ≤ 0.001). Eighty percent (16/20) of goat herds and 60% (24/40) of sheep flocks had at least one seropositive animal (p ≥ 0.05). The average within goat herds and sheep flock seroprevalence were 36.4% (ranged: 0-91%) and 23.4% (ranged: 0-82%), respectively. Multivariate logistic regression model revealed that seroprevalence increased 1.79 times in goat herds compared with sheep flocks, 3.2 times more in farms containing ≥ 100 animals, and 1.7 times higher in farms with their animals that were ≥ 2 years of age than in farms with their animals that are < 2 years of age. In addition, seroprevalence significantly increased 1.52 times in farms loaning bucks or rams during breeding season and 1.63 times in farms containing cats on premises (p ≤ 0.05). Farm biosecurity measures are essential to prevent introduction and minimize transmission of C. burnetii infection to humans and animals.