Introduction Cervical kinesthesia is an important part of movement control and of great importance for daily function. Previous research on kinesthesia in whiplash-associated disorders (WAD) has focused on grades I-II. More research is needed on WAD grade III. The aim of this study was to investigate cervical kinesthesia in individuals with WAD grades II-III before and after a neck-specific exercise intervention and compare them to healthy controls. Methods A prospective, case-control study with a treatment arm (n = 30) and a healthy control arm (n = 30) was conducted in Sweden. The WAD group received a neck-specific exercise program for 12 weeks. The primary outcome to evaluate kinesthesia was neck movement control (the Fly test). Secondary outcomes were neck disability, dizziness and neck pain intensity before and after the Fly test. Outcomes were measured at baseline and post-treatment. The control arm underwent measurements at baseline except for the dizziness questionnaire. A linear mixed model was used to evaluate difference between groups (WAD and control) and over time, with difficulty level in the Fly test and gender as factors. Results Between-group analysis showed statistically significant differences in three out of five kinesthetic metrics (p = 0.002 to 0.008), but not for the WAD-group follow-up versus healthy control baseline measurements. Results showed significant improvements for the WAD-group over time for three out of five kinaesthesia metrics (p < 0.001 to 0.008) and for neck disability (p < 0.001) and pain (p = 0.005), but not for dizziness (p = 0.70). Conclusions The exercise program shows promising results in improving kinesthesia and reducing neck pain and disability in the chronic WAD phase. Future research might benefit from focusing on adding kinesthetic exercises to the exercise protocol and evaluating its beneficial effects on dizziness or further improvement in kinesthesia. Impact statement Kinesthesia can be improved in chronic WAD patients without the use of specific kinesthetic exercises.