A National Olympic Committee (NOC) could enter up to 3 qualified cyclists in the cross-country. Quota places are allocated to the NOC, which selects the cyclists. Qualification is primarily through the UCI nation rankings, with 30 of the 38 quota places available through that pathway. The top 2 NOCs earned 3 quota places. NOCs ranked 3rd through 7th earned 2 quota places. NOCs ranked 8th through 21st earned 1 quota places. The second path to qualification was continental tournaments for Africa, the Americas, and Asia; the top NOC at each tournament (which had not already earned a quota place) received 1 place. The third path was the 2019 UCI Mountain Bike World Championships. The top 2 NOCs (without a quota place yet) in the Elite category earned a place; the top 2 NOCs in the U-23 category (without a quota, including through the Elite category) also earned a place. The host nation was reserved one place, to be reallocated through the rankings if Japan earned a place normally. Because qualification was complete by the end of the 2020 UCI Track Cycling World Championships on 1 March 2020 (the last event that contributed to the 2018–20 rankings), qualification was unaffected by the COVID-19 pandemic.