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Small mammals, such as rodents and shrews, are natural reservoir hosts of zoonotic diseases, including parasitic protozoa. To assess the risk of rodent-borne parasitic protozoa in the Republic of Korea (ROK), this study investigated the status of parasitic protozoa, namely <i>Trypanosoma</i>, <i>Babesia</i>, and <i>Theileria</i>, in small mammals. In total, 331 blood samples from small mammals were analyzed for parasites using PCR and sequenced. Samples were positive for <i>Trypanosoma grosi</i> (23.9%; <i>n</i> = 79) and <i>Babesia microti</i> (10%; <i>n</i> = 33) but not <i>Theileria</i>. Small mammals from Seogwipo-si showed the highest infection rate of <i>T. grosi</i> (48.4%), while the highest <i>B. microti</i> infection rate was observed in those from Gangneung-si (25.6%). Sequence data revealed <i>T. grosi</i> to be of the AKHA strain. Phylogenetic analysis of <i>B. microti</i> revealed the US and Kobe genotypes. <i>B. microti</i> US-type–infected small mammals were detected throughout the country, but the Kobe type was only detected in Seogwipo-si. To our knowledge, this is the first nationwide survey that confirmed <i>T. grosi</i> and <i>B. microti</i> infections at the species level in small mammals in the ROK and identified the Kobe type of <i>B. microti</i>. These results provide valuable information for further molecular epidemiological studies on these parasites.