There seems to be no information on the incidence of injury and associated risk factors for academy football players in Ghana. We determine the risk factors associated with match and training injuries among male football players at an academy in Ghana. Preseason measurements of players’ height, weight, and ankle dorsiflexion (DF) range of motion (ROM) were measured with a stadiometer (Seca 213), a digital weighing scale (Omron HN-289), and tape measure, respectively. The functional ankle instability (FAI) of players was measured using the Cumberland Ankle Instability Tool (CAIT), and dynamic postural control was measured with the Star Excursion Balance Test. Injury surveillance data for all injuries were collected by resident physiotherapists throughout one season. Selected factors associated with injury incidence were tested using Spearman’s rank correlation at a 5% significance level. Age was negatively associated with overall injury incidence (r = − 0.589,p= 0.000), match (r = − 0.294,p= 0.008), and training incidence (r = − 0.314,p= 0.005). Previous injury of U18s was associated with training injuries (r = 0.436,p= 0.023). Body mass index (BMI) was negatively associated with overall injury incidence (r = − 0.513,p= 0.000), and training incidence (r = − 0.395,p= 0.000). CAIT scores were associated with overall injury incidence (n = 0.263,p= 0.019) and match incidence (r = 0.263,p= 0.029). The goalkeeper position was associated with match incidence (r = 0.241,p= 0.031) while the U16 attacker position was associated with training incidence. Exposure hours was negatively associated with overall injury incidence (r = − 0.599,p= 0.000). Age, BMI, previous injury, goalkeeper and attacker positions, ankle DF ROM, and self-reported FAI were associated with injury incidence among academy football players in Ghana.