Potato has become one of the staple crops to improve food security in North Korea since the late 1990s. However, the potato yield has been stagnated around 11–12 t ha−1 for several decades, and a food shortage is still a primary issue in North Korea. Yield gap analyses were carried out using the SUBSTOR-potato model to quantify the potato yield gaps and explore the potential ways to close the yield gaps in two different cropping seasons in North Korea (early- and main-season potatoes). Yield gaps were estimated to be around 80% for both early- and main-season potatoes. Early-season potato yield was substantially determined by water or nitrogen supplies, depending on the year’s weather condition (i.e., with or without spring drought). Irrigation during the vegetative stage could effectively reduce the year-to-year variation in yield as well as the yield gap (+7.0 t ha−1, +66.1%). Meanwhile, additional nitrogen fertilizer in the early-season potatoes was less effective compared to that in the main-season potatoes. For the main-season potatoes, where precipitation was sufficient, the primary limiting factor of yield was nitrogen supply. Since heavy rainfall aggravated nitrogen leaching, additional nitrogen fertilizer is recommended as a top dressing rather than a basal dressing. Additional top dressing at 50 days after planting with the current amount of nitrogen fertilizer was expected to increase the main-season potato yield by 42.0 t ha−1 (+191.4%). This study highlights that the primary limiting factor of potato yield may differ between the cropping seasons. Therefore, our findings suggest that different agronomic strategies should be applied for different cropping seasons to improve potato production in North Korea, where agronomic resources are limited.