Each year, whiplash injuries from motor vehicle collisions (MVC) affect millions worldwide, with no strong evidence of pathology. While the majority recover soon after the injury, the same is not true for roughly 20% reporting higher levels of pain and distress, without diagnostic options. This study used magnetization transfer (MT) imaging to quantify white matter integrity in 78 subjects with varying levels of pain, 1 year after MVC. MT images of the cervical spinal cord were collected parallel to the intervertebral disks. MT ratios (MTR) were calculated in select white matter tracts along with MTR homogeneity (MTRh) at each level. Significant differences were observed between clinical outcome groups in the left and right spinothalamic tracts (p = 0.003 and 0.020) and MTRh (p = 0.009). MTRh was elevated in females with poor recovery versus females reporting recovery (p < 0.001) or milder symptoms (p < 0.001), and in males reporting recovery (p = 0.007) or no recovery (p < 0.001). There was a significant interaction between recovery status and sex (p = 0.015). MT imaging identified tract specific and regional changes in white matter integrity suggesting potential insults to the cord. Additionally, significant MTRh differences between sexes were observed, characterizing the heterogeneity of whiplash recovery and worse outcomes in females.