Mosquitoes serve as vectors of important human pathogens, such as dengue, yellow fever, West Nile and chikungunya viruses. Investigating the mosquito response to viral infection will help in understanding disease transmission and in turn may provide novel strategies to prevent disease outbreaks. To identify differentially expressed transcripts, Illumina-based high-throughput RNA-sequencing was performed on mock-infected and West Nile virus (WNV)-infected Culex quinquefasciatus (Hsu) cells. Initially, the reads were assembled using de novo transcriptome assembler, Trinity, allowing identification of novel transcript isoforms. Analysis by Expectation-Maximization (RSEM) for transcript abundance estimation and R/Bioconductor packages showed 440 genes to be differentially regulated by infection. Reference-based method using Tuxedo software package was also used and analysis using cuffdiff-R/cummeRbund package identified 235 differentially expressed genes. Pathway analysis was performed using Ingenuity software to predict the localization and function of the transcripts shared by the two separate methods. The RNA-seq results were validated using real-time RT-PCR. The results will provide a basis for further characterization of various processes involved in mosquito cells after viral infection.