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Chickpea (<i>Cicer arietinum</i> L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in <i>Cicer</i> is lacking. In this study, we acquire high-throughput transcriptome sequencing data and analyze changes in gene expression during floral transition in the early flowering cultivar ICCV 96029, later flowering <i>C. arietinum</i> accessions, and two wild species, <i>C. reticulatum</i> and <i>C. echinospermum</i>. We identify <i>Cicer</i> orthologs of <i>A. thaliana</i> flowering time genes and analyze differential expression of 278 genes between four species/accessions, three tissue types, and two conditions. Our results show that the differences in gene expression between ICCV 96029 and other cultivated chickpea accessions are vernalization-dependent. In addition, we highlight the role of <i>FTa3</i>, an ortholog of <i>FLOWERING LOCUS T</i> in <i>Arabidopsis</i>, in the vernalization response of cultivated chickpea. A common set of differentially expressed genes was found for all comparisons between wild species and cultivars. The direction of expression change for different copies of the <i>FT-INTERACTING PROTEIN 1</i> gene was variable in different comparisons, which suggests complex mechanisms of FT protein transport. Our study makes a contribution to the understanding of flowering time control in <i>Cicer</i>, and can provide genetic strategies to further improve this important agronomic trait.