Abstract Background Involvement in a compensation process following a motor vehicle collision is consistently associated with worse health status but the reasons underlying this are unclear. Some compensation systems are hypothesised to be more stressful than others. In particular, fault-based compensation systems are considered to be more adversarial than no-fault systems and associated with poorer recovery. This study compares the perceived fairness and recovery of claimants in the fault-based compensation system in New South Wales (NSW) to the no-fault system in Victoria, Australia. Methods One hundred eighty two participants were recruited via claims databases of the compensation system regulators in Victoria and NSW. Participants were > 18 years old and involved in a transport injury compensation process. The crash occurred 12 months (n = 95) or 24 months ago (n = 87). Perceived fairness about the compensation process was measured by items derived from a validated organisational justice questionnaire. Health outcome was measured by the initial question of the Short Form Health Survey. Results In Victoria, 84 % of the participants considered the claims process fair, compared to 46 % of NSW participants (χ2 = 28.54; p < .001). Lawyer involvement and medical assessments were significantly associated with poorer perceived fairness. Overall perceived fairness was positively associated with health outcome after adjusting for demographic and injury variables (Adjusted Odds Ratio = 2.8, 95 % CI = 1.4 – 5.7, p = .004). Conclusion The study shows large differences in perceived fairness between two different compensation systems and an association between fairness and health. These findings are politically important because compensation processes are designed to improve recovery. Lower perceived fairness in NSW may have been caused by potential adversarial aspects of the scheme, such as liability assessment, medical assessments, dealing with a third party for-profit insurance agency, or financial insecurity due to lump sum payments at settlement. This study should encourage an evidence informed discussion about how to reduce anti-therapeutic aspects in the compensation process in order to improve the injured person’s health.