The aim of this study was to investigate the seroprevalence of Q fever in sheep and goats in Kasur, Okara, and Pakpattan in the Punjab of Pakistan. Q fever is a widely reported zoonotic disease caused by Coxiella (C.) burnetii. The main reservoirs are small ruminants that excrete the bacteria in birth by-products in high numbers. Thus, the bacteria can also be detected in the air and the dust of livestock farms. The infection is often asymptomatic in ruminants, but it can lead to reproductive disorders. This cross-sectional study found that a significant number (n = 43; 11.3%) of 300 randomly selected small ruminants of nine tehsils were seropositive using a commercially available ELISA. Seroprevalence was significantly higher in goats (17.1%) than in sheep (4.9%). Binary logistic regression analysis proved that species, age, and breed have a significant effect on the prevalence of Q fever. Tick infestation, contact with animal fomites, contact with other animals, production system, and health status of an animal had a significant impact on the prevalence of Q fever. These findings on Q fever in animals can be used to improve the visibility of this zoonotic disease. These findings will help local health authorities to focus on the origin of the problem and facilitate applying preventive measures to the affected livestock farms.