Background: Over the past few decades, CrossFit has become a very popular physical activity. However, there is little literature on its effect, as resistance training, on the performance of soccer players. Objective: This study examined the effects of 12 weeks of CrossFit training on muscular strength, speed, agility, and VO 2max in young male soccer players. Methods: Thirty-eight soccer players were divided randomly into the experimental group (n = 19, age 17.32 ± 1.02 years, body height 1.76 ± 0.15 m, body mass 63.24 ± 5.68 kg, body mass index 21.34 ± 1.32 kg/m 2 ) and control group (n = 19, age 17.21 ± 1.70 years, body height 1.74 ± 0.16 m, body mass 63.43 ± 5.21 kg, body mass index 21.45 ± 1.21 kg/m 2 ). Both groups underwent 12 weeks of the usual soccer training program, including physical exercises on a regular basis, three times a week. Additionally, in the experimental group, a training program based on high-intensity functional physical activity was added during each training session as part of the usual weekly training regimen. Pre-and post-intervention tests were performed to measure player performance, including 30-m sprint, Yo-Yo intermittent recovery test level 1, vertical jump, agility T-test, sit-ups, and push-ups during 60 s. Results: A significant group x time effect was found for all tests: 30-m sprint (p = .012, η p 2 = .42), Yo-Yo test (p = .029, η p 2 = .23), vertical jump (p = .002, η p 2 = .46), T-test (p = .002, η p 2 = .21), sit-ups (p < .001, η p 2 = .55), push-ups (p = .001, η p 2 = .25). The improvement was higher in the experimental group for all variables. Conclusions: CrossFit training is an effective strategy for improving the physical capacities in young soccer players.