Coxiellosis caused by Coxiella burnetii is a cosmopolitan zoonosis, which causes significant losses through abortions and stillbirths in small ruminants. A cross-sectional seroprevalence study was conducted in two major sheep and goat farming districts of Punjab (Layyah and Muzaffargarh), Pakistan. In total, 542 small ruminants (271 sheep and goats each) of both sexes (60 males and 482 females) of different age groups from 104 flocks (52 flocks of either species) were randomly selected for the collection of sera and related epidemiological information. The sampling plan was devised at the expected prevalence of 50%, confidence interval (CI) of 95%, and error margin of 5%. A commercial indirect enzyme-linked immunosorbent assay (iELISA; ID Vet) was used to test the samples for the presence of both phase I and II antibodies. A high herd level prevalence (73.1%, 95% CI 63.5-81.3) was recorded in the studied districts. Individual level seroprevalence was recorded as 30.8% (95% CI 26.9-34.9). Higher value was recorded in females (32%) when compared with males (21.7%). Higher prevalence (34.8%, 95% CI 21.4-50.2) was observed in animals of 1 year (nulliparous) than to primiparous (24.8%, 95% CI 17.4-33.5) and multiparous (32.3%, 95% CI 27.6-37.3) animals. Univariable analysis indicated that caprine species (odds ratio [OR] 1.96, p = 0.22), females (OR = 1.70, p = 0.104), infestation with ticks (OR = 234.39, p < 0.001), abortion history (OR 1.96, p = 0.14), retention of fetal membranes (OR 1.50, p = 0.35), keeping a single breed in a herd (OR 1.50, p = 0.56), and mixed feeding management (OR 1.37, p = 0.33) were the variables found associated with high prevalence of antibodies to C. burnetii. The study indicates that seroprevalence of coxiellosis was high in the studied small ruminant population and further studies are required to discern its epidemiology more precisely.