Long-term symptoms after whiplash injury often comprise neck pain, headache, anxiety, depression, functional impairment and low quality of life. In an observational cohort study, we examined physical and mental health effects in patients with subacute to chronic whiplash-associated disorders (WAD) after participation in a multimodal rehabilitation (MMR) program. MMR is a team-based multi-professional method based on a bio-psycho-social model with a cognitive focus to reach an individualized and common goal for the team and patient together. Standardized self-report questionnaires were filled in three times: before MMR, after MMR, and one year after MMR. A total of 322 participants completed the program, 161 of whom responded in full and were further analyzed. At one-year follow-up after MMR, a significant improvement was seen in the evaluation of the primary outcomes (physical and mental health) and secondary outcomes (anxiety, depression, pain intensity and interference with life). Women improved on all outcomes while men did not improve on the psychological measures (mental health, depression and anxiety). This study indicates that a MMR program could be beneficial for patients with subacute to chronic WAD, at least for women, since the outcomes at one-year follow-up were positive.