Functional assessments identify biomechanical issues which may indicate risk for injury and can be used to monitor functional recovery after an injury or surgery. Although the gold standard to assess functional movements is marker-based motion capture systems, these are cost prohibitive and have high participant burden. As such, this study was conducted to determine if a markerless motion capture system could detect preinjury differences in functional movements between those who did and did not experience a noncontact lower extremity injury (NCLEI). A three-dimensional markerless motion capture system comprised an area of 3 m × 5 m × 2.75 m was used. Participants were Division I collegiate athletes wearing plain black long-sleeve shirts, pants, and running shoes of their choice. Functional assessments were the bilateral squat, right and left squat, double leg drop vertical jump, static vertical jump, right and left vertical jump, and right and left 5 hop. Measures were recorded once and the first NCLEI was recorded during the first year after measurement. Two-factor analysis of variance models were used for each measure with factors sex and injury status. Preinjury functional measures averaged 8.4 ± 3.4 minutes capture time. Out of the 333 participants recruited, 209 were male and 124 were female. Of those, 127 males (61%) and 92 females (74%) experienced later NCLEI. The most common initial NCLEI was nonanterior cruciate ligament knee injury in 38 females (41.3%) and 80 males (62.0%). Females had decreased flexion and lower valgus/varus displacement during the bilateral squat (p < 0.006). In addition, knee loading flexion for those who were not injured were more than that seen in the injured group, and was more pronounced for injured females (p < 0.03). The markerless motion capture system can efficiently provide data that can identify preinjury functional differences for lower extremity noncontact injuries. This method holds promise for effectively screening patients or other populations at risk of injury, as well as for monitoring pre-/postsurgery function, without the large costs or participant burden.