Background: The impact of the COVID-19 pandemic on the incidence of notifiable infectious diseases (NID) in Taiwan remains unclear. Methods: The number of cases of NID between January and September 2019 and 2020 were obtained from the open database established by the Taiwan Centers for Disease Control for comparison. Percentage change was defined as the difference in the number of cases between 2020 and 2019, divided by the number in 2019 and multiplied by 100. Findings: Overall, 42 NID were included in this study. The number of cases was 21,895 between January and September 2020, which was lower than the number of cases during the same period in 2019 (n = 24,469), with a decline in incidence from 102.9 to 91.7 per 100,000 people in 2019 and 2020, respectively. Among these diseases, 30 infectious diseases showed a lower incidence in 2020 than in 2019. In contrast, an increase in the number of cases of 10 diseases was observed in 2020 in comparison with 2019, and 2 diseases had the same number of cases in both 2019 and 2020. Fourteen airborne/droplet, 11 fecal-oral, seven vector-borne, and four direct-contact transmitted NID had an overall reduction of 2,700 (-28.1%), 156 (-23.0%), 557 (-54.8%), and 73 (-45.9%) cases, respectively, from 2019 to 2020. Similar trends were observed for the changes in incidence, which were 11.5 (-28.4%), 6.7 (-23.4%), 2.4 (-55.0%), and 0.3 (-46.2%) per 100,000 people for airborne/droplet, fecal-oral, vector-borne, and direct-contact transmitted NID, respectively. In addition, all the 38 imported NID showed a reduction of 632 (-73.5%) cases from 2019 to 2020. In contrast, 4 sexually transmitted diseases (STDs) showed an increase of 903 (+7.2%) cases from 2019 to 2020, which was attributed to the increase in gonorrhea (from 3,220 to 5,028). The overall incidence of STDs increased from 52.5 to 56.0 per 100,000 people, with a percentage change of +6.7%. Interpretation: This study demonstrated a collateral benefit of COVID-19 prevention measures for various infectious diseases, except STDs, in Taiwan, during the COVID-19 epidemic.Funding Statement: This study did not receive any specific funding from agencies in the public, commercial, or not-for-profit sectors.Declaration of Interests: The authors have no competing interests.