Groin pain syndrome (GPS) is a prevalent issue in soccer. This study assessed the effectiveness of a new preventive protocol on GPS for youth soccer players. The protocol included targeted stretching and strengthening exercises for the adductor and core muscles from preseason to midseason. A questionnaire and two pain provocation tests were used for the evaluation. Mild GPS required positive results in at least two evaluations, while severe GPS was associated with pain incompatible with engagement in any activity confirmed by diagnostic ultrasound. Forty-two elite male athletes (aged 16.9 ± 0.7 years) participated in the study, with half of them assigned to the usual training (control group) and the remaining athletes undergoing the preventive protocol (treatment group) for 24 weeks. GPS rates were 14.3% (three diagnoses: two mild, one severe) in the treatment group and 28.6% (six diagnoses: three mild, three severe) in the control group. Toward the end of the season, three players, one from the treatment group and two from the control group had to stop playing due to severe GPS problems. In addition, one player in the control group stopped midseason. Even though the reduction in the risk of developing GPS was not significant (relative risk of 0.50 ([95%CI 0.14 to 1.74], = 0.2759), the halved incidence of severe GPS and the increased muscle strength related to the treatment ( = 0.0277) are encouraging data for future studies.