Fat body from Anopheles stephensi female mosquitoes were dissected and processed for proteomic analysis. Both SDS-PAGE and basic Reverse Phase Liquid Chromatography-based fractionation strategies were used to achieve a broad coverage of protein identification. The fractionated peptides were then analyzed on a high-resolution mass spectrometer. Searching the raw data against the protein database of An. stephensi resulted in identification of 4535 proteins, which is, to our knowledge, the largest catalog of fat body proteome in any mosquito vector species reported so far. Bioinformatics analysis on these fat body proteins suggested the enrichment of biological processes including carbon and lipid metabolism, amino acid metabolism, signal peptide processing and oxidation-reduction. In addition, using proteogenomic approaches, 43 novel proteins were identified, which were not listed in the annotated gene annotations of An. stephensi. The data used in the analysis are related to the article 'Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes' (Prasad et al., 2017).