This study aimed to explore the application value of two laboratory tests in the diagnosis of Epstein-Barr virus-associated infectious mononucleosis (EBV-IM) in children. From January 2018 to December 2020, 166 patients with EBV-IM were included in this study. Two methods were used in the analysis. The results of both tests were compared and analyzed. The age of onset of EBV-IM is mainly distributed in the range of 0-6 years, and no difference by gender is observed. The sensitivity and specificity of EBV testing by PCR were 49.4% and 89.8%, respectively, and the area under the receiver operating characteristic curve (AUC) was 0.714 (0.662-0.762). When using the immunofluorescence method to detect EBV antibodies, the two indices with the highest diagnostic efficacy were low-affinity EBV-CA IgG and EBV-CA IgM, and their AUC values were 0.798 (0.751-0.840) and 0.663 (0.609-0.713), respectively. When combining the two indices for testing, the AUC values of EBV-CA IgM + low-affinity EBV-CA IgG, EBV-DNA+EBV-CA IgM, and EBV-DNA+low-affinity EBV-CA IgG were 0.904 (0.867-0.933), 0.768 (0.719-0.812), and 0.963 (0.937-0.981), respectively. The diagnostic efficacy of the combined EBV-DNA+EBV-CA IgM + low-affinity EBV-CA IgG test was optimal compared with that of a single index or the combination of two indices, with an AUC of 0.999 (0.986-1.000; p < 0.05), sensitivity of 100%, and specificity of 89.8%. The combined immunofluorescence and real-time PCR methods have high sensitivity and specificity and good application value in the clinical diagnosis of EBV-IM.