Hamstring injuries are one of the most prevalent injuries in rugby union and many other running-based sports, such as track sprinting and soccer. The majority of these injuries occur during running; however, the relationship between running mechanics and hamstring injury is unclear. Obtaining large samples of prospective injury data to examine this relationship is difficult, and therefore exploratory analysis frameworks may assist in deriving valuable information from studies with small but novel samples. The aim of this study was to undertake a prospective exploratory analysis of the relationship between running mechanics and hamstring injury. Kinematic and kinetic data of the trunk, pelvis and lower limbs were collected during maximal overground running efforts for ten elite rugby union athletes. Subsequently, hamstring injury occurrence was recorded for the following Super Rugby season, during which three athletes sustained a running-based hamstring injury. Functional principal component analysis was used to visualise patterns of variability in running mechanics during the late swing phase between athletes. Results indicated that subsequently injured athletes demonstrated a tendency for greater thoracic lateral flexion, greater hip extension moments and greater knee power absorption, compared to uninjured athletes. All variables demonstrated an ability to descriptively differentiate between injured and uninjured athletes at approximately 60% of the late swing phase. Therefore, we hypothesize that greater thoracic lateral flexion, a greater hip extension moment and greater knee power absorption between peak hip flexion and peak knee extension during the late swing phase may put rugby athletes at greater risk of running-based hamstring injury.