“Clicker training” is a popularly promoted training method based on operant conditioning with the use of a secondary reinforcer (the clicker). While this method draws from theories of learning and is used widely, there has been little scientific investigation of its efficacy. We used 60 horses, Equus callabus, and assigned each horse to one of six reinforcement protocols. The reinforcement protocols involved combinations of reinforcers administered (primary versus secondary plus primary), schedule of reinforcement (continuous versus variable ratio), and reinforcers applied during extinction (none or secondary). There were no differences (P≥0.11) between horses which received a secondary reinforcer (click) followed by the primary reinforcer (food) and those which received only the primary reinforcer (food) in the number of trials required to train the horses to touch their noses to a plastic cone (operant response). There also were no differences (P≥0.12) between horses which received the secondary reinforcer plus primary reinforcer and those which received only the primary reinforcer in regards to the number of trials to extinction. We conclude that there is no difference in the amount of training required to learn the operant task or in the task’s resistance to extinction between horses that received a secondary reinforcer followed by a primary reinforcer versus horses which received only a primary reinforcer.