The cation/proton antiporter (CPA) family represents a class of transmembrane transporter proteins that play a crucial role in plants during high salinity stress by maintaining the cell’s ionic balance and pH homeostasis. So far, the CPA genes have not been systematically characterized in tomato (Solanum lycopersicum). In this study, we identified and analyzed 33 putative CPA genes in tomato. Phylogenetic analysis showed that tomato CPAs could be classified into three subgroups, i.e., CHX (18 genes), KEA (8 genes), and NHX (7 genes). CPA genes within each subgroup shared similar motifs, conserved catalytic domains and gene structure. Further analysis revealed that the CPA genes were unevenly distributed on the chromosomes and segmental duplication events played a major role in the expansion of the CPA gene family in tomato. Gene expression analysis exhibited that CPA genes were differentially expressed in different tissues, various stages of fruit development, and differentially regulated in response to abiotic stresses, especially salt stress. Further, co-localization of tomato CPA genes with quantitative trait loci (QTL) of salt stress-related phenotypes revealed their broader functions in salt stress tolerance. Finally, predicted protein–protein interactions of tomato CPAs, gene ontology analysis, and the presence of putative cis-elements in the promoter further support the diverse role of tomato CPAs in plant development and plant stress tolerance. In brief, this study highlights the potential role of tomato CPAs in plant development and abiotic stress tolerance, especially in salt stress, and provides comprehensive information to explore new candidate genes for salt tolerance in tomato.