Purpose: The aim of the present study is to examine the performance of young Japanese cross-country skiers of different competitive levels with the use of Yo-Yo tests and the 12-minute run test (12MRT) that have been demonstrated to be related to each level, and to know which test is suitable for different competitive performance. Methods: Elite group (N = 9) was 16.9 ± 0.3 years and moderate trained group (N = 22) was 16.1 ± 0.9 years. The testing sessions consisted of the following: 1) Vertical jump and 50m sprint; 2) the Yo-Yo tests level 1 and 2 (intermittent recovery); 3) 12MRT. Results: Results showed the vertical jump heights and 50m sprint that no significant both performances differences were found among the two groups. Significant the Yo-Yo tests and 12MRT performances differences were found between the two groups (p < 0.05). Performance test (%) showed the ratio of moderate trained group towards elite group. The Yo-Yo tests performance was low enough compared with the result of 12MRT in moderate trained group. Conclusions: It is therefore valid to assume that low Yo-Yo tests performance due to immature anaerobic in cross-country skiers was a new limiting factor in the competitive level.