Chikungunya virus (CHIKV), causing Chikungunya fever (CF), is transmitted by Aedes mosquitoes primarily in tropical regions.CHIKV infection poses a public health burden owing to international travel and climate change.Implementation of Next-generation sequencing (NGS) for whole-genome sequencing (WGS) contributes to the formulation of effective public health and travel medicine policies to mitigate emerging CHIKV in non-endemic areas.A patient with CF, who traveled to Thailand, was enrolled at Sacred Chuncheon Hospital (Chuncheon, Republic of Korea).Amplicon-based NGS was performed using the patient's sera on days 2 and 6 after hospitalization.The nearly whole genome sequence of CHIKV was recovered from day 2 post-hospitalization, while only 9% on day 6.The phylogenetic inference demonstrated that the CHIKV genotype belonged to the East/Central/South African lineage.In addition, zoonotic potential was evaluated by the machine learning model.This study highlights the effectiveness of amplicon-based MinION sequencing derived from a patient who traveled from an endemic area.Collection of patient samples early in infection is strongly correlated with genomic acquisition and genotypic identification.Therefore, this study provides insight into the active surveillance for NGS-based genomic diagnosis and characterization of emerging CHIKV outbreak in endemic and non-endemic areas.