Astragalus sikokianus is a rare Japanese perennial of the seashore that was reported to be extinct in the wild. The small seed size and deep dormancy of A. sikokianus make it difficult for direct seeding restoration in aspects of seed handling, transport, planting, and seedling establishment. For the large-scale economic restoration of dormant small-seeded species, seed pelleting combined with the breaking of dormancy was studied. Physiological (prechilling and plant hormones) and physical (hot water, hydrochloric acid, and sulfuric acid) seed dormancy break treatments were evaluated. The dormant broken seeds were used for pelleting. The effects of the substrate, pellet sizes, and their interactions on germination were measured. The scarification of five rubs of seeds placed between sandpapers completely broke the physical dormancy of A. sikokianus. Seed coat impermeability inhibited germination. Pelleted seeds ranging from 2.0 to 4.0 mm in diameter showed more than 90% germination on filter paper. The germination of the pelleted seeds was measured in commercial, field, and sand soil conditions. The highest germination was shown in sand (70–74% GP), regardless of the pellet size, whereas unpelleted scarified seeds germinated only 48%. These results suggest that small-seeded species with physical dormancy can be used for seed-based restoration after seed pelleting.