Zika virus (ZIKV) is a recently emerged arbovirus which has rapidly spread throughout the Americas since 2015. The virus is mainly transmitted by the mosquito vector, Aedes aegypti, which is also the principle vector of dengue virus. Due to the recent emergence of the virus, there is very little known about its interaction with the vector at the molecular level. In this project, we embarked on RNA-Seq analyses of coding as well as non-coding RNAs from infected and non-infected mosquitoes. Analysis of short-interfering RNAs showed that the mosquito elicits an RNAi response against the virus, and alterations in the abundance of a large number of coding and non-coding RNAs occurs. Interestingly, the altered microRNAs showed overlaps with those observed in other flavivirus infections, but not those of alphaviruses. Transcriptome analysis showed that overall, the transcript levels of 1332 genes were altered at 2, 7 and 14 days post-ZIKV infection by 2-fold or more, with most of the changes occurring at 7 days post-infection. These were mostly involved in metabolic process, cellular process and proteolysis. In addition, 486 long intergenic non-coding RNAs showed changes upon ZIKV infection, 80 of which overlapped with that of dengue virus infected mosquitoes. Overall, the results provide a global overview of transcriptional responses of Ae. aegypti to ZIKV infection, which help us to gain a better understanding of pro and anti-viral mosquito factors.