Clusters of acute upper respiratory tract infections are mainly caused by type A or B influenza virus. Numerous factors modify the risk of upper respiratory tract infection (URTI) cluster transmission. The purpose of this study was to investigate the epidemiological characteristics, differences, and epidemic trends in influenza viruses and in non-influenza respiratory pathogens, and the distribution of the sites of URTI cluster events in Taiwan from 2011 to 2019. We examined the publicly available annual summary data on 1864 confirmed URTI clusters in the Taiwan Centers for Disease Control (Taiwan CDC) from 2011 to 2019. URTI clusters were mainly divided into 1295 clusters of influenza virus infections, 149 clusters of non-influenza respiratory pathogen infections, 341 clusters of pathogens not detected by routine tests, and 79 clusters of unchecked samples. There were statistically significant differences (p < 0.001) in the event numbers of URTI clusters among influenza and non-influenza respiratory pathogens between 2011 and 2019. There were statistically significant differences (p = 0.01) in instances of URTI clusters among non-influenza respiratory pathogens between 2011 and 2019. There were also statistically significant differences (p < 0.001) in instances of URTI clusters in different locations between 2011 and 2019. In all the pathogens of URTI clusters (odds ratio (OR) = 1.89−2.25, p = 0.002−0.004), most single infections were influenza A viruses (64.9%, 937/1444). Respiratory syncytial virus single infections were most numerous (43.0%, 64/149) among the non-influenza respiratory pathogens of URTI clusters. Of the institutions where URTI clusters occurred, schools had the most cases (50.1%, 933/1864) (OR = 1.41−3.02, p < 0.001−0.04). After the categorization of isolated virus strains by gene sequencing, it was found that, of the seasonal influenza A viruses, the H1N1 subtype viruses were predominantly A/California/07/2009, A/Michigan/45/2015, and A/Brisbane/02/2018, and the H3N2 subtype viruses were predominantly A/Hong Kong/4801/2014, A/Singapore/INFIMH-16−0019/2016, and A/Switzerland/8060/2017, during 2017−2019. Of the influenza B viruses, B/Brisbane/60/2008 (B/Vic) was the dominant type, and some were B/Massachusetts/02/2012 (B/Yam) and B/PHUKET/3073/2013 (B/Yam). This study is the first report of confirmed events of URTI clusters from surveillance data provided by the Taiwan CDC (2011−2019). This study highlights the importance of long-term, geographically extended studies, particularly for highly fluctuating pathogens, for understanding the implications of the transmission of URTI clusters in Taiwanese populations. Knowledge gaps and important data have been identified to inform future surveillance and research efforts in Taiwan.