Limited understanding exists regarding clinical distinctions between influenza A/H3N2 and A/H1N1 subtypes, particularly in primary health care. We conducted a comparative analysis of symptomatic characteristics of influenza subtypes in Korea. This retrospective study analyzed medical records of patients who presented with positive test results for influenza-like illness (rapid influenza diagnostic test; RIDT) during the H3N2-dominant 2016-2017 and H1N1-dominant 2018-2019 seasons. Symptomatic manifestations, contact history, vaccination history, and clinical course were analyzed between the two seasons. The most frequent symptom in the RIDT-positive patients was fever (80.1% and 79.1%, respectively). The average body temperature was higher, and the number of patients with high fever was greater in the H3N2-dominant season than in the H1N1-dominant season (p < 0.001). Conversely, other symptoms, such as myalgia, cough, and sore throat, were significantly more common in the H1N1-dominant season than in the H3N2-dominant season (p < 0.001). Antiviral drugs were prescribed to most febrile RIDT-positive patients (82.2% and 81.3%, respectively, p = 0.516). Analyzing primary care data revealed different clinical manifestations according to the subtype. Therefore, physicians should consider these variable hallmarks and employ tailored therapeutic strategies to reduce the complication rate.