Current evidence on the effectiveness and safety of Chuna manipulative therapy (CMT) for managing non-acute lower back pain (LBP) is insufficient. We investigated the comparative effectiveness and safety of CMT, a Korean style of manipulation, plus usual care (UC) compared to UC alone for non-acute LBP. We conducted a parallel, two-armed, multi-centered, assessor blinded, pragmatic, randomized controlled trial at four major Korean medical hospitals. Overall, 194 patients were randomly allocated to either CMT plus UC (n = 97) or UC alone (n = 97), for six weeks of treatment and six months follow-up. The primary outcome was measured using the numerical rating scale (NRS) of LBP intensity at 7 weeks. Secondary outcomes included NRS of leg pain, Oswestry Disability Index (ODI) for functional disability, patient global impression of change (PGIC) scale, and safety. A total of 194 patients were included in the intention-to-treat analysis, and 174 patients provided complete data for the primary outcome. At 7 weeks, clinically significant differences between groups were observed in the NRS of LBP (CMT + UC: −3.02 ± 1.72, UC: −1.36 ± 1.75, p < 0.001), ODI scores (CMT + UC: −5.65 ± 4.29, UC: −3.72 ± 4.63, p = 0.003), NRS of leg pain (CMT + UC: −2.00 ± 2.33, UC: −0.44 ± 1.86, p < 0.0001), and PGIC (CMT + UC: −0.28 ± 0.85, UC: 0.01 ± 0.66, p = 0.0119). Mild to moderate safety concerns were reported in 21 subjects. CMT plus UC showed higher effectiveness compared to UC alone in patients with non-acute LBP in reducing LBP and leg pain and in improving function with good safety results using a powered sample size and including mid-term follow-up.