Japanese encephalitis virus (JEV) constitutes a persistent public health concern in Japan. Despite the prevalence of potential JEV vectors, Aedes albopictus Skuse and Culex pipiens form molestus Forskål, their competence within the Japanese mosquito population remains unexplored. This study aimed to assess the role of these two mosquito species, incorporating an analysis of insect-specific virus (ISV) infection status to comprehensively understand vector competence assessment. Mosquito colonies were initially screened by high-throughput sequencing to determine their natural infection of ISV and subsequently exposed to JEV genotype I and III. Evaluation points, including infection rate (IR), dissemination rate (DR), and transmission efficiency (TE) were analyzed to define vector competency, and respective ISV statuses such as Culex flavivirus (CxFV) and Aedes flavivirus were investigated post-JEV exposure. We found that both species could transmit JEV, albeit at a distinct rate of TE, i.e., ∼61% and ∼11% in Ae. albopictus and Cx. p. molestus. The presence of ISVs in the studied mosquito colonies generally showed no statistically significant impact on JEV vector competence; nonetheless, experiments employing Cx. p. molestus showed a lower DR at 7 dpi in CxFV-infected colonies compared to CxFV-free colonies. In conclusion, our findings suggest that both Japan-originated mosquito species have the capability to infect and transmit JEV genotypes 1 and 3, while the virome appears to exert no influence on this phenotype. While positive and negative interactions between ISV and arbovirus have been described in many studies, further investigations are necessary to fully comprehend the mechanism behind these interactions.