Background: Non-specific neck pain and headache are major economic and individual burden in office-workers. The aim of this study is to investigate the effect of a multi-component intervention combining workstation ergonomics, health promotion information group workshops, neck exercises, and an app to enhance intervention adherence to assess possible reductions in the economic and individual burden of prevalent and incident neck pain and headache in office workers. Methods/design: This study is a stepped wedge cluster-randomized controlled trial. Eligible participants will be any office-worker aged 18-65 years from two Swiss organisations in the Cantons of Zurich and Aargau, working more than 25 h a week in predominantly sedentary office work and without serious health conditions of the neck. One hundred twenty voluntary participants will be assigned to 15 clusters which, at randomly selected time steps, switch from the control to the intervention group. The intervention will last 12 weeks and comprises workstation ergonomics, health promotion information group workshops, neck exercises and an adherence app. The primary outcome will be health-related productivity losses (presenteeism, absenteeism) using the Work Productivity and Activity Impairment Questionnaire. Secondary outcomes are neck disability and pain (measured by the Neck Disability Index, and muscle strength and endurance measures), headache (measured by the short-form headache impact test), psychosocial outcomes (e.g. job-stress index, Fear-Avoidance Beliefs Questionnaire), workplace outcomes (e.g. workstation ergonomics), adherence to intervention, and additional measures (e.g. care-seeking). Measurements will take place at baseline, 4 months, 8 months, and 12 months after commencement. Data will be analysed on an intention to treat basis and per protocol. Primary and secondary outcomes will be examined using linear mixed-effects models. Discussion: To the authors' knowledge, this study is the first that investigates the impact of a multi-component intervention combining current evidence of effective interventions with an adherence app to assess the potential benefits on productivity, prevalent and incident neck pain, and headache. The outcomes will impact the individual, their workplace, as well as private and public policy by offering evidence for treatment and prevention of neck pain and headache in office-workers.