The development of improved rootstock and its commercialization have revolutionized the production of fruit crops worldwide. Rootstocks can influence biotic and abiotic stress tolerance, yield, tree vigour control, precocity, crop load, and improve fruit quality. But breeding of rootstocks, particularly for perennial fruit crops, is challenging because it requires almost double the time than scion breeding and so many desirable traits are required to be combined into a hybrid progeny. The increased breeding activity of rootstock breeders is the reason why a wide range of new rootstocks are available today. However, breeding rootstocks for fruit crops is much slower than scion breeding within the same species. As new breeding techniques specifically target the desired gene or traits, marker assisted selection and genetic editing methods like RNA interference, cisgenesis, transgrafting, etc., open up new possibilities for rootstock breeders and enable them to develop superior rootstocks. Genetic engineering techniques have been employed to introduce specific genes into rootstocks, providing resistance against diseases, tolerance to abiotic stresses, and improved nutrient uptake. This review provides a comprehensive overview of the advancements in breeding techniques and their challenges which will help in planning future research and innovation in rootstock breeding.