Korean pine (Pinus koraiensis Sieb. et Zucc.) is a critical coniferous species ecologically. In addition, its fruits have numerous nutraceutical properties and its wood is high quality timber. However, this plant has a low propagation rate and is under risk of extinction. To accelerate breeding of the excellent seedlings and selection from Korean pine, determining methods to increase the number of Korean pine trees successfully is imperative. In this present study, using sprouted seeds as the initial explants, the de novo organogenesis system for this coniferous species has been successfully developed. After 30 days of incubation on Gupta and Durzan (DCR) medium containing 2 mg L−1 kinetin (KT) and 0.5 mg L−1 thidiazuron (TDZ), 92.67% of explants produced direct buds with an average of about 15 buds per explant. We confirmed the organogenic regeneration pattern by a scanning electron microscopy (SEM). For bud elongation after 60 days of culture, we obtained the highest mean length of 34.99 mm on DCR basal media supplemented with 6-benzyladenine (6-BA, 0.2 mg L−1), 1-naphthaleneacetic acid (NAA, 0.1 mg L−1), and activated charcoal (AC, 1 g L−1). The highest rooting rates of 20.74 and 21.48% were obtained within two months of culturing on 1/2 DCR medium (halved major elements) supplemented with 0.05 mg·L−1 NAA and 0.5 or 1 mg ·L−1 indole-3-butyric acid (IBA), respectively. Rooted shoots showed a survival rate of 90.28% after acclimatization in the substrate consisting of perlite, peat, and vermiculite (1:1:1). This protocol is a successful and efficient biotechnological approach to the micropropagation of Korean pine, and the results will be helpful to the clonal propagation and conservation of Korean pine.