Abstract Background Depressive disorders are highly prevalent in the working population and are associated with excessive costs for both society and companies. Effective treatment for employees with depressive symptoms in occupational health care is limited. The purpose of this study is to investigate the effectiveness and cost-effectiveness of an indicated preventive web-based guided self-help course for employees with depressive symptoms. Methods The study is a two-arm randomized controlled trial comparing a web-based guided self-help course with care-as-usual. The self-help course consists of 6 weekly lessons. Weekly support will be provided by a coach via the website. Subjects in the care-as-usual group do not receive any treatment in addition to regular care. 200 white collar workers from several national and international companies in the Netherlands will be recruited via different methods such as banners on the company’s intranet, pamphlets and posters. Subjects will be included when they: have elevated depressive symptoms (score ≥16 on the Center for Epidemiologic Studies Depression scale), are 18 years of age or older, have access to the Internet and can be contacted via e-mail. Exclusion criteria are: partial or full work absenteeism, a legal labor dispute with the employer and receiving treatment from the company’s occupational health care at study entrance. The primary outcome is depressive symptoms. Secondary outcomes include work absenteeism, work performance, burnout, anxiety, quality of life, health care use and production losses. Outcome data will be collected at 8 weeks, 6 months, and 12 months after baseline. Analyses will be based on the intention-to-treat principle. The cost-effectiveness analyses will be performed from a societal and a company’s perspective. A process evaluation will be conducted alongside the study. Discussion This study evaluates the effectiveness and cost-effectiveness of a web-based guided self-help course for employees with depressive symptoms. This study could stimulate the use of e-mental health interventions in the worksite setting. Trial registration Nederlands Trial Register (NTR): TC2993