Cefquinome is primarily used in veterinary medicine for the treatment of bacterial infections in animals, especially in cattle and pigs. It is effective against a wide range of Gram-positive and Gram-negative bacteria, making it a valuable option for treating respiratory infections in calves and pigs. It is commonly administered to manage bovine respiratory disease (BRD), where pathogens like Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni are involved. In swine, it is used to treat infections caused by Actinobacillus pleuropneumoniae and other susceptible organisms associated with respiratory disease.

Due to its broad-spectrum activity and rapid bactericidal action, cefquinome is often chosen in cases where quick control of severe infections is needed. Its formulation allows for convenient once-daily dosing, improving compliance in farm settings. It is not used in humans and is restricted to veterinary use to preserve the effectiveness of cephalosporins in human medicine.