(1) Objective: To analyze the exercise programs used to prevent of acute hamstring injuries in eleven-a-side football players, and their effectiveness. (2) Methods: A systematic review (PRISMA) was conducted (2008–2020), including RCTs, that exclusively used physical exercises as a prevention method. (3) Results: Ten studies were selected considering 14 interventions, including nine different programs: FIFA11+ (11+), Harmoknee, eccentric Nordic Hamstring Exercise (NHE) exclusively, with eccentric exercises, with stretching or with proprioceptive, New Warm-up Program (NWP), Bounding Exercise Program (BEP), the only one with no positive results, and proprioceptive exercises. Incidence of injuries and strength were the most considered variables, both with favorable evidences. Programs including NHE, which assessed injury incidence, were always effective. The 11+ program was effective in injury incidence and strength; NWP was effective in balance, stability, and strength. (4) Conclusions: The exercise programs discussed were effective to prevent acute hamstring injuries in football players except BEP and partially Harmoknee. Exercises mostly used to reduce the risk of hamstring injuries are those of eccentric force due to its functionality, especially NHE. Only concentric contractions and isometric contractions obtained significant favorable results. The most complete and promising programs were 11+ (in injury incidence and strength) and NWP (strength, balance, and stability). NWP was the best in strength.