High-quality movement patterns and high levels of mindfulness are thought to be beneficial in preventing sports injuries. Yoga is recommended in the field of athlete rehabilitation. This study investigated the effects of yoga intervention on functional movement patterns and mindfulness in collegiate athletes. It is a quasi-experimental study with a pre/post-test control design. The participants were divided into a yoga group and a control group. A Functional Movement Screen and the Mindful Attention Awareness Scale were used to assess participants’ basic movement patterns and mindfulness before and after 12 weeks of yoga intervention (two classes per week, 90 min per class). The results show that the yoga group’s FMS scores improved more compared to the control group [F(1,78) = 29.08, p < 0.001, ŋp2 = 0.27], and that the scores for the deep squat (ŋp2 = 0.4), shoulder mobility (ŋp2 = 0.17), and trunk stability pushup (ŋp2 = 0.36) improved substantially. The dysfunctional score ratio for deep squats (χ2 = 18.57, p < 0.001), shoulder mobility (χ2 = 26.90, p < 0.001), trunk stability pushup (χ2 = 17.07, p < 0.001), and rotatory stability (χ2= 38.29, p <0.001) decreased significantly compared with the control group, but there was no significant improvement in asymmetric movement patterns (χ2 = 0.75, p = 0.39). The mindfulness scores in the yoga group significantly exceeded those of the control group [F(1,78) = 13.56, p < 0.001, ŋp2 = 0.15]. These results suggest that yoga intervention can improve functional movement patterns and mindfulness levels, but further evidence is needed to determine whether yoga could positively influence sports injuries.