Porcine circovirus 3 (PCV-3) is an emerging circovirus species that has recently been reported in different countries around the world, suggesting a widespread circulation. In this study, sera samples originating from 654 pigs of different production phases and clinical/pathological conditions, submitted for diagnostic purposes between 1996 and 2017, were randomly selected. Detection of PCV-3 genome in such samples was attempted with a previously described PCR method, and the partial genome sequence was obtained from selected PCV-3-positive samples from different years. Compiled data confirmed that PCV-3 has been circulating in the Spanish pig population since 1996. The overall frequency of PCV-3 PCR-positive samples in the study period was 11.47% (75 of 654). Phylogenetic analysis of twelve PCV-3 partial sequences obtained showed a high nucleotide identity with the already known PCV-3 sequences, with minor variations among years. No significant correlation was found between the detection of PCV-3 and any production phase nor clinical/pathological condition. These results confirm PCV-3 circulation at least since 1996 in the Spanish pig population with a low/moderate frequency. Although the information obtained was limited, PCV-3 did not appear to be linked to any specific pathological condition or age group.