Background <p>This study examined the acute effects of four structured warm-up protocols “FIFA 11+”, PEP, HarmoKnee, and a “dynamic warm-up” on phase-specific countermovement jump (CMJ) performance and neuromuscular activation patterns in elite youth soccer players.</p> Methods <p>Nineteen male athletes (15.1 ± 0.1 years) completed each protocol in a randomized crossover design, with CMJ analysis focusing on the eccentric, concentric, and landing phases. Kinematic (knee joint angles), kinetic (peak vertical ground reaction forces), and electromyographic (EMG) measurements of the vastus lateralis (VL) and semitendinosus (ST) activation were synchronized during CMJ execution.</p> Results <p>FIFA 11 + demonstrated superior acute effects across all CMJ phases: during the eccentric braking phase, eliciting greater knee flexion angles (p &lt; 0.05) and higher VL pre-activation. The concentric propulsion phase showed a 12.6% greater peak force (1434.63 ± 175.86 N vs. 1340.31 ± 135.99 N after dynamic warm-up, p = 0.001) and 11.2% higher jump height (35.95 ± 1.89 cm vs. 31.92 ± 1.64 cm, p = 0.011); during landing, there was a 24.9% greater impact force absorption (4331.99 ± 128.73 N vs. 3468.05 ± 96.19 N, p &lt; 0.001) with more balanced ST activation. EMG analysis revealed FIFA 11 + protocol induced significantly higher muscle activation than other protocols throughout all CMJ phases (VL: 21–28% increase; ST: 18–25% increase; both p &lt; 0.01), particularly during the eccentric-concentric transition phase (0.20 ± 0.03 s vs. 0.28 ± 0.04 s after dynamic warm-up).</p> Conclusion <p>These phase-specific enhancements suggest that the FIFA 11 + protocol enhances the neuromuscular system for rapid force production and absorption more effectively than other warm-up routines. The findings support the use of structured neuromuscular warm-ups for optimizing acute performance, although future longitudinal studies should examine their cumulative effects on injury prevention.</p>