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Simple Summary: Vitamin D is a fat-soluble prohormone crucial for bone mineralization, muscle contractility, and neurological conductivity. It is theorized that Vitamin D plays an important role in sport performances, especially in young athletes. In this study we examined the associations of levels of 25-hydroxyvitamin D (25(OH)D) with physical fitness and motor-performance achievements in youth soccer players from Southern Croatia. Participants were tested on physical fitness, motor performance and vitamin D at the end of the winter period, when levels of vitamin D are known to be lowest due to low exposure to sunlight. Results showed that deficiency of 25(OH)D was widespread among youth soccer players living in Southern Croatia. Low 25(OH)D levels were associated with lower results in fitness tests (i.e., tests of energetic capacities), but there was no correlation between 25(OH)D levels and the results in motor performance tests (i.e., skill tests). Our results support the theory of the association between vitamin D and energetic capacities of athletes, but there is no evidence on association between vitamin D and skill-based capacities. Vitamin D level is known to be a factor potentially influencing physical fitness, but few studies have examined this phenomenon among youth athletes. We aimed to evaluate the associations of vitamin D levels (as measured by 25-hydroxyvitamin D concentrations—25(OH)D) with various physical fitness and motor performance tests in youth football (soccer) players. This cross-sectional study included a total of 52 youth soccer players (15.98 ± 2.26 years old) from Southern Croatia. The participants were evaluated at the end of the winter period and data were collected of anthropometric measures (body mass and body height), vitamin D status (25(OH)D levels), physical fitness tests (sprints of 10 and 20 m, 20 yards test, the countermovement jump, the reactive strength index (RSI)) and motor performance tests (the soccer-specific CODS, the soccer-specific agility, and static balance). Among the studied players, 54% had 25(OH)D insufficiency/deficiency, showing a lack of 25(OH)D is widespread even in youth athletes living at a southern latitude. The 25(OH)D level was correlated with sprint 20 m, 20 yards tests, and RSI, showing a greater role of 25(OH)D in physical fitness tests where energetic capacity is essential than in sport-related motor performance tests where skills are crucial. Our results support the idea that vitamin D can play a determinant role in physical fitness tests with a clear physiological component, but is not crucial in motor performance tests related to specific sports where skills are a key component. Future studies should investigate the effects of vitamin D supplementation on the performance in physical fitness and motor performance tests among youth athletes. [ABSTRACT FROM AUTHOR]