Zika virus has been circulating in Thailand since 2002 through continuous but likely low-level circulation. Here, we describe an infection in a pregnant woman who travelled to Thailand and South America during her pregnancy. By combining phylogenetic analysis with the patient's travel history and her pregnancy timeline, we confirmed that she likely got infected in Thailand at the end of the year 2021. This imported case of microcephaly highlights that ZIKV circulation in the country still constitutes a health risk, even in a year of lower incidence.