This is the first cost-effectiveness analysis of Chuna manual therapy (CMT) plus usual Korean traditional medicine for traffic accident victims using a randomized controlled trial. A total of 132 participants were equally allocated to the intervention group receiving 6–11 sessions of CMT plus usual Korean traditional medicine care for three weeks or usual care including acupuncture, cupping, herbal medicine, moxibustion, and traditional physiotherapy at three hospitals. At 12 weeks, from a healthcare perspective, the intervention group had significantly higher costs (mean (SD), $778 (435) vs. $618 (318); difference, $160; 95% CI, $15 to $289; p = 0.005). From a societal perspective, total costs were insignificantly lower in the intervention group (mean (SD), $1077 (1081) vs. $1146 (1485); difference, $−69; 95% CI, $−568 to $377; p = 0.761). The intervention group dominated, with significantly higher QALYs gained at lower overall cost with a 72% chance of being cost-effective. From a societal perspective, the intervention was cost-saving for individuals who had neck pain after car accidents, although it was not cost-effective from the healthcare perspective ($40,038 per QALY gained). Findings support use of CMT as an integrated care treatment for whiplash from a societal perspective. Further studies with larger sample sizes are needed to determine cost-effectiveness in other cultural contexts.