CrossFit^®, a high-intensity functional training program, places considerable physical demands on athletes and may contribute to musculoskeletal injuries. Understanding injury patterns and risk factors is essential for developing prevention strategies. This study investigated injury prevalence, types, and associated risk factors among Czech CrossFit^® practitioners and examined the impact on training routines. A cross-sectional online survey was distributed to athletes training for at least six months at licensed affiliates across the Czech Republic. Descriptive statistics summarized participant characteristics and injuries. Chi-square and t-tests compared groups, and logistic regression estimated odds ratios (ORs) for risk factors including age, sex, CrossFit^® experience, and weekly training volume. Of 456 athletes (214 men and 242 women), 36.4% reported at least one injury in the past six months. The most injured areas were the spine (30.7%), shoulder (28.3%), and palm (14.5%). Snatches, box jumps, deadlifts, cleans, and pull-up variations accounted for most injuries. Overuse injuries were most prevalent (49.2%). Injured athletes were younger (p = 0.008) and trained more hours per week (p = 0.046). Logistic regression showed that increasing age (OR = 0.97; 95% CI: 0.94–0.99; p = 0.032) and absence of competitive participation (OR = 0.61; 95% CI: 0.39–0.96; p = 0.039) reduced injury risk. These findings highlight the substantial impact of injuries on training and support targeted prevention strategies—such as skill progression, load management, and appropriate scaling—to promote safer long-term participation in CrossFit^®.