Pigeon pea is a multipurpose food legume cultivated predominantly in semiarid tropics and subtropics of Asia, Africa, and Latin America. It is the second most important pulse crop of India. Pigeon pea breeding is primarily centered around enhancing its biotic stress tolerance/resistance, and improvement of plant ideotype for traits like determinacy, earliness, and photosensitivity and toward development of high yielding hybrids. In the last few decades, a number of improved varieties have been developed through conventional breeding approaches but practical yield realized from these cultivars has still remained below the potential yield. Additionally, the time required to develop a new variety through conventional breeding is major constraint. Hence, integration of advanced genomics technologies is essential to produce high-yielding, stress-tolerant cultivars in the shortest possible time. Over the past few decades, pigeon pea genomic resources have been enriched with whole genome sequences along with germplasm resequencing and transcriptomics data. Genomic resources have been utilized for genome-wide molecular markers discovery, deciphering marker/gene–trait associations and development of high-throughput genotyping assays. Molecular characterization of germplasm and diverse mapping populations has led to the creation of a dense genetic maps, identification of quantitative trait loci (QTLs) and biotic and abiotic stress tolerance genes. The progress in modern breeding tools, including genomic selection, sequence-based breeding, and speed breeding, coupled with the availability of cost-effective high-throughput genotyping and automated phenotyping facilities, is poised to revolutionize pigeon pea crop improvement programs in the future.