We report the first identification of Zika virus in Pakistan following genomic and serological analyses of blood samples from 20 patients with febrile illness. In November 2021, an outbreak of dengue-like illness occurred in the metropolitan city of Karachi. Viral genome capture and sequencing of seven patients revealed six cases of dengue virus serotype 2 and two Zika virus infections, including one dengue and Zika virus co-infection. The next year, following severe flooding, 13 suspected dengue patients were screened by real time qRT-PCR and serology, and 92% (12/13) had evidence of current or recent Zika virus infection. Phylogenetic analyses revealed the Zika viruses originated from Brazil. The most recent observed ancestor dates to 2016, suggesting a prior importation event and ongoing circulation. Our results suggest that Zika virus may be circulating and contributing to disease burden during seasonal Dengue outbreak.