Introduction: There is paucity of research regarding the incidence of hamstring injuries and its inherent causes within youth Malaysian football contexts. We aim to investigate the incidence of hamstring injuries among youth footballers and analyse the risk between intrinsic risk variables (anthropometric and hip strength) and the risk of hamstring strain injuries (HSI). Materials and methods: This was a prospective cohort study involving 72 youth Malaysian professional footballers from a single prestigious club. This study was conducted during the 2023 Malaysian football league. Pre-season medical evaluations encompassed demographic information, anthropometric measurements, and isometric strength examinations of the hamstrings, quadriceps, hip abductors, and hip adductors. Injury surveillance was conducted during the season. Results: The incidence of HSI in this study was 0.331 injuries per 1000 H, with incidence of injury during match higher 2.79 injuries per 1000 H compared to training 0.216 injuries per 1000 H. There was no hamstring injuries reported in U20. Forty-one (56.9%) has hamstring to quadriceps (H:Q) ratio <0.6 and forty-six (63.9%) has hip abductor to adductor ratio <0.8. The binary logistic regression analysis revealed increasing age (OR: 1.227, CI: 0.98 – 5.03), increased body mass index (OR: 1.79, CI: 0.415 – 7.77), increased body fat mass (OR: 1.39, CI: 0.33 – 5.89), and low H:Q ratio (OR: 4.274, CI: 0.347 – 58.1), increase the risk of HSI. Conclusion: Injury prevention programs in youth footballers should incorporate these modifiable risk factors into account to reduce the risk of hamstring injuries.