Although small-scaled breeding programs for apples, pears, and grapes were conducted in the 1930s and 1940s, national fruit breeding programs by the Korean government were commenced after the foundation of the National Horticultural Technical Institute on May 20, 1953, and the programs were confined to apples and pears. Peach and grape breeding programs were started after the establishment of Rural Development Administration (RDA), with the Horticultural Experiment Station as its affiliated research organization in 1962. However, because of insufficiencies in breeding infrastructure, manpower, and funds during the 1960s and 1970s, most efforts were devoted to the collection and selection of wild Akebia and Actinidia, local varieties of astringent persimmons, jujube, and apricot, and adaptability tests of foreign fruit varieties. Fruit breeding programs became more activate with the establishment of the Apple Research Institute, the Pear Research Institute and the Citrus Research Institute as subsidiary organizations of the Fruit Research Institute, RDA, in 1991, and with Fruit Experiment Stations for grapes, persimmons, and peaches as affiliated provincial research organizations in early 1990s to cope with the domestic agricultural market opened by Uruguay Round Agreements. The legislation of the Seed Industry Law in 1995 and joining the UPOV in 2002 contributed to fruit breeding activation in the private sector. The results of such breeding programs include the development of the ‘Danbae’ pear as the first fruit variety in 1967, the ‘Yumyong’ peach in 1977, the ‘Hongro’ apple, and the ‘Cheongsoo’ grape. After the Korea-Chile FTA, effective in 2004, research projects for the development of molecular markers linked to disease resistance in fruit trees and seedless grapes have been carried out to improve the competitiveness of the Korean fruit industry. However, the establishment of a molecular breeding system based on genome sequence information and collaboration among research organizations are required for competition in domestic and foreign fresh fruit markets. In this review, we analyze the achievement from the fruit breeding programs operated by central and local autonomous governments since 1945, and propose future directions and strategies.