Various biological constraints including erratic and asynchronous flowering between male and female plants hinder successful hybrid development and genetic gains in greater yam breeding programs. Therefore, pollen storage has gained much attention to facilitate artificial pollinations and increase the genetic gains. This 4-year study aimed at developing a practical long-term pollen storage technique for the successful development of yam hybrids. Fresh pollens were collected from two Dioscorea alata males, then lyophilized (two lyophilization treatments were applied), followed by storage at room temperature (24°C–25°C) for 12 months. Moreover, the lyophilized and stored pollens were tested for viability by crossing with four female varieties. Our results showed that lyophilization is effective for achieving viable pollens after 12 months of storage. Treatment 1 (48 h drying) showed higher pollen germination and fertility rates than Treatment 2 (72 h drying). Although we observed a reduction in viability of lyophilized pollens after 12 months of storage, we generated hybrid seedlings with success rates from 12% to 21% compared to 21%–31% when using fresh pollens. Paternity testing based on molecular genotyping confirmed the hybrid status of the obtained seedlings, which grew well in a greenhouse. Lyophilization is a practical approach for a long-term storage of greater yam pollen samples. This protocol will positively impact yam breeding programs particularly in developing countries.