Summary Background Back pain remains a challenge for primary care internationally. One model that has not been tested is stratification of the management according to the patient's prognosis (low, medium, or high risk). We compared the clinical effectiveness and cost-effectiveness of stratified primary care (intervention) with non-stratified current best practice (control). Methods 1573 adults (aged ≥18 years) with back pain (with or without radiculopathy) consultations at ten general practices in England responded to invitations to attend an assessment clinic. Eligible participants were randomly assigned by use of computer-generated stratified blocks with a 2:1 ratio to intervention or control group. Primary outcome was the effect of treatment on the Roland Morris Disability Questionnaire (RMDQ) score at 12 months. In the economic evaluation, we focused on estimating incremental quality-adjusted life years (QALYs) and health-care costs related to back pain. Analysis was by intention to treat. This study is registered, number ISRCTN37113406. Findings 851 patients were assigned to the intervention (n=568) and control groups (n=283). Overall, adjusted mean changes in RMDQ scores were significantly higher in the intervention group than in the control group at 4 months (4·7 SD 5·9 vs 3·0 5·9, between-group difference 1·81 95% CI 1·06–2·57) and at 12 months (4·3 6·4 vs 3·3 6·2, 1·06 0·25–1·86), equating to effect sizes of 0·32 (0·19–0·45) and 0·19 (0·04–0·33), respectively. At 12 months, stratified care was associated with a mean increase in generic health benefit (0·039 additional QALYs) and cost savings (£240·01 vs £274·40) compared with the control group. Interpretation The results show that a stratified approach, by use of prognostic screening with matched pathways, will have important implications for the future management of back pain in primary care. Funding Arthritis Research UK.