A cluster-randomized controlled trial, WorkUp, was conducted for working-aged patients at risk of sick leave or on short-term sick leave due to acute/subacute neck and/or back pain in Sweden. The purpose of WorkUp was to facilitate participants to stay at work or in case of sick leave, return-to-work. The aim of this study was to study whether the WorkUp trial was cost-effective. Patients in the intervention and reference group received structured evidence-based physiotherapy, while patients in the intervention group also received a work place dialogue with the employer as an add-on. The participants, 352 in total, were recruited from 20 physiotherapeutic units in primary healthcare in southern Sweden. The economic evaluation was performed both from a healthcare and a societal perspective with a 12-month time frame with extensive univariate sensitivity analyses. Results were presented as incremental cost-effectiveness ratios (ICER) with outcomes measured as quality-adjusted life-years (QALY) and proportion working for at least 4 weeks in a row without reported sick leave at 12-month follow-up. From the healthcare perspective, the ICER was €23,606 (2013 price year) per QALY gain. From the societal perspective the intervention was dominating, i.e.. less costly and more effective than reference care. Bootstrap analysis showed that the probability of the intervention to be cost-effective at €50,000 willingness-to-pay per QALY was 85% from the societal perspective. Structured evidence-based physiotherapeutic care together with workplace dialogue is a cost-effective alternative from both a societal and a healthcare perspective for acute/subacute neck and/or back pain patients.Trial registration ClinicalTrials.gov: NCT02609750.