Background: Cytomegalovirus (CMV) is a highly specific herpes virus spreading only from person to person. Valganciclovir (VGCV) and ganciclovir (GCV) are effective in the treatment of neonatal congenital CMV infection. Objectives: This study aimed to compare the curative effects of VGCV and GCV among neonates with CMV infection and evaluate their effects on hearing. Methods: A total of 48 neonates with congenital CMV infection admitted to Huaian Maternal and Child Health Care Hospital, China, were selected from January 2016 to December 2019 and randomly divided into two equal groups of intervention and group (n = 24 each). While the control group received intravenous injection of GCV, the intervention group received oral VGCV. After a 6-week course of treatment, polymerase chain reaction (PCR) was applied to detect the CMV load in both urine and blood. We used the ELISA method to detect the serum CMV-IgM expression level before and after treatment. Moreover, we compared the positive rates of CMV-DNA and CMV-IgM, hyperbilirubinemia, retinitis, hepatosplenomegaly, thrombocytopenia, neutropenia, as well as the results of hearing screening and brainstem auditory evoked potentials (BAEP). Results: Before treatment, there was no statistical difference in blood/urine CMV-DNA expression level and positive expression rates of blood/urine CMV-DNA and CMV-IgM between the groups (P > 0.05). After treatment, blood/urine CMV-DNA expression and the positive expression rates of blood/urine CMV-DNA and CMV-IgM significantly decreased in both groups compared to before treatment (P < 0.05), but there was no statistical significance between the two groups (P > 0.05). Before treatment, there was no significant difference in hearing abnormality rates between the control (50%) and intervention (62.5%) groups (P > 0.05). After treatment, both the control (20.83%) and intervention (29.17%) groups had significantly decreased hearing abnormality rates, and the difference was statistically significant compared with before treatment (P < 0.05), but the difference between the two groups was not statistically significant (P > 0.05). After treatment, the results of comparing BAEP showed that both groups had no statistically significant differences in the number of neonates with normal hearing, mild hearing loss, moderate to severe hearing loss, severe hearing loss, and extremely severe hearing loss (P > 0.05). Before treatment, both groups had no statistically significant differences in the number of neonates with hyperbilirubinemia, retinitis, hepatosplenomegaly, thrombocytopenia, and neutropenia (P > 0.05). After treatment, while the number of neonates with hyperbilirubinemia, retinitis, hepatosplenomegaly, and thrombocytopenia decreased, neutropenia cases increased, and the difference before and after treatment was statistically significant (P < 0.05); however, the difference between the two groups was not statistically significant (P > 0.05). Conclusions: VGCV is similar to GCV in the treatment of neonatal congenital CMV infection, but the oral route of administration of VGCV is more acceptable among neonates.