Background: Equine Coital Exanthema (ECE) is an endemic herpesvirus disease primarily affecting the external genitalia and impairing mating functions in horses. Its extremely contagious nature, latency, and subclinical features can result in outbreaks and significant economic losses. The primary transmission pathway of the disease is through mating activities; therefore, robust biosecurity measures are crucial in breeding facilities. Objectives: This study aims to determine the clinical prevalence of ECE among horses in a covering station in Türkiye from 2021 to 2024. It also aims to assess the efficacy of routine PCR implementation within ECE’s control strategies. Study design: A cross-sectional study design has been employed. Methods: Genital swab samples were collected from clinically suspected horses, which were tested for EHV-3 using real-time PCR. Animal records, clinical examination data, and PCR test results were obtained from horses at the covering station between 2021 and 2024. Results: During the 4 years (2021-2024), 9231 mating activities were carried out, and a total of 228 clinically suspected horses were tested for EHV-3 using real-time PCR. Among these 228 horses, 6 horses (2.6%) were confirmed positive for EHV-3. Main limitations: The primary weakness of this study is the failure to detect subclinical instances with PCR. Conclusions: The molecular diagnosis of ECE was reported for the first time in Türkiye. Clinical ECE instances infrequently transpired over the four-year period at the covering station. No epidemic transpired during this interval. PCR testing plays a crucial role in disease control when implemented with suitable management methods. Additional global epidemiological investigations on ECE are required.