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Chikungunya virus (CHIKV) is an emerging pathogen around the world and causes significant morbidity in patients. A single amino acid mutation in the envelope protein of CHIKV has led to a shift in vector preference towards <i>Aedes</i> <i>albopictus</i>. While mosquitoes are known to mount an antiviral immune response post-infection, molecular interactions during the course of infection at the tissue level remain largely uncharacterised. We performed whole transcriptome analysis on dissected midguts of <i>Aedes albopictus</i> infected with CHIKV to identify differentially expressed genes. For this, RNA was extracted at two days post-infection (2-dpi) from pooled midguts. We initially identified 25 differentially expressed genes (<i>p</i>-value &lt; 0.05) when mapped to a reference transcriptome. Further, multiple differentially expressed genes were identified from a custom <i>de novo</i> transcriptome, which was assembled using the reads that did not align with the reference genome. Thirteen of the identified transcripts, possibly involved in immunity, were validated by qRT-PCR. Homologues of seven of these genes were also found to be significantly upregulated in <i>Aedes aegypti</i> midguts 2 dpi, indicating a conserved mechanism at play. These results will help us to characterise the molecular interaction between <i>Aedes albopictus</i> and CHIKV and can be utilised to reduce the impact of this viral infection.