Abstract Background Bopivirus B is an emerging picornavirus that affects goats in China. This study aimed to establish a TaqMan real-time PCR assay for detecting Bopivirus B and conduct a preliminary survey of infection in six goat farms in Sichuan province, China. Specific primers and a probe targeting the 3D gene of Bopivirus B were designed, and the TaqMan-based real-time PCR assay was successfully established following the optimization of reaction conditions and components. A total of 257 goat fecal samples were collected from six farms in Sichuan and tested using the newly developed method. Results The assay demonstrated a linear relationship between 2.73 × 103 and 2.73 × 109 copies/µL, with a high correlation coefficient (R2 = 0.999) and amplification efficiency of 109%. Additionally, the assay exhibited excellent specificity and reproducibility, with a detection limit of 27.3 copies/µL. The field positive rate of Bopivirus B was 100%, and a higher positive rate was observed in diarrheal fecal samples (33.72%) compared to non-diarrheal fecal samples (12.28%, P