This is a pragmatic, two-armed, parallel, single-center, randomized controlled clinical trial for comparative evaluation between the effectiveness of integrated Korean medicine (IKM) and herbal medicine treatment with that of IKM monotherapy (control) for post-accident syndrome persistent after the acute phase. Participants were randomized into Herbal Medicine (HM, n = 20) and Control groups (n = 20) to receive the allocated treatment of 1–3 sessions/week for 4 weeks. Intention-to-treat analysis was conducted. The Difference of Numeric Rating Scale (NRS) change of overall post-accident syndromes from baseline to week 5 for the two groups was 1.78 (95% CI: 1.08–2.48; p < 0.001). Regarding secondary outcomes, a significant decrease compared to the baseline values was confirmed for NRS of musculoskeletal, neurological, psychiatric complaints and general symptoms of post-accident syndromes. In a survival analysis based on the recovery criteria of “patients with a reduction in the NRS of overall post-accident syndromes of ≥50%,” the HM group showed a shorter time to recovery than the control group during the 17-week study period (p < 0.001 by the log-rank test). IKM combined with herbal medicine treatment significantly improved the quality of life by relieving somatic pain and alleviating the overall post-accident syndrome persistent after the acute phase; this effect was maintained for at least 17 weeks.