Human bocavirus (HBoV) has been identified as a viral agent with a global presence, especially in young patients with gastrointestinal infections. In this study, we aimed to evaluate the epidemiological patterns of the HBoVs associated with acute gastroenteritis (AGE) in Taiwan. A total of 2994 AGE fecal samples from several diarrhea outbreaks from 2018 to 2022 were analyzed. From the samples, 73 positive samples were detected in three different bocaviruses: 30 (41.1%) were from HBoV1; 37 (50.7%) were from HBoV2; and 6 (8.2%) were from HBoV3, revealing the respective prevalences in AGE of 1%, 1.2%, and 0.2%. HBoV1 and HBoV2 were the two major epidemic agents of HBoVs in Taiwan during this study period and have seasonal distinct patterns with an epidemic peak from October to the following March. Phylogeny reconstruction and evaluation were implemented in Mega X; the results revealed that most HBoV1 strains in Taiwan appeared to be closely related to those strains from other Asian countries. The HBoV2 exhibited substantial genetic diversity and the HBoV3 genes showed discordance of groups.