Coxiellosis (Q-fever) caused by Coxiella burnetii is a cosmopolitan zoonosis that causes significant losses through abortions and stillbirths in small ruminants. A cross-sectional seroprevalence study was conducted in three agricultural zones of Borno State in the flocks of sheep and goats. Seven hundred sixty-eight small ruminants (384 sheep and goats each) of both sexes (282 males and 486 females) of different age groups from 90 flocks were randomly selected to collect sera and related epidemiological data information. A commercial indirect enzyme-linked immunosorbent assay (iELISA; I.D. Vet) was used to test the samples for the presence of both phases I and II antibodies to Coxiella burnetii infections. The seroprevalence in sheep and goats was 10.9% (44/384) and 12.0% (46/384). There was no statistically significant association in the two species of the animals tested and the infection rates of coxiellosis. Bivariate analysis showed that female animals of all species tested were more seropositive for antibodies to Coxiella burnetii than males. There was a statistically significant association between the sex of both sheep and goats tested and the infection rates of coxiellosis. Breed and age of sheep and goats were not statistically significant for seropositivity to Coxiella burnetii. The study indicates that seroprevalence of coxiellosis was high in the studied small ruminants’ population, particularly among female sheep and goats and can be considered a potential risk for both susceptible animals and humans in the study area.