Background Internet- and mobile based stress-management interventions (iSMI) may be an effective means to address the negative consequences of occupational stress. However, available results from randomised controlled trials are conflicting. Moreover, it is yet not clear whether guided or unguided self-help iSMI provide better value for money. Internet-based mental health interventions without guidance are often much less effective than interventions including at least some guidance from a professional. However, direct comparisons in randomised controlled trials are scarce and, to the best of our knowledge, the comparative (cost)-effectiveness of guided vs. unguided iSMI has not yet been studied. Hence, this study investigates the acceptability and (cost-) effectiveness of minimal guided and unguided iSMI in employees with heightened levels of perceived stress. Methods A three-armed randomised controlled trial (RCT) will be conducted to compare a minimal guided and unguided iSMI with a waiting list control condition (WLC). Both active conditions are based on the same iSMI, i.e. GET.ON Stress, and differ only with regard to the guidance format. Employees with heightened levels of perceived stress (PSS ≥ 22) will be randomised to one of three conditions. Primary outcome will be comparative changes in perceived stress (PSS). Secondary outcomes include changes in self-reported depression, work-engagement, presenteeism and absenteeism. Moreover, a cost-effectiveness analysis will be conducted from a societal perspective, including both direct medical costs and costs related to productivity losses. In addition, a cost-benefit analysis will be conducted from the employer’s perspective. Incremental net-benefit regression analyses will address the question if there are any baseline factors (i.e. subgroups of employees) associated with particularly favorable cost-effectiveness when the experimental intervention is offered. Assessments take place at baseline, 7 weeks post-treatment and 6 months after randomisation. Discussion Online-based (guided) self-help interventions could be an acceptable, effective and economically sustainable approach to offer evidence-based intervention alternatives to reduce the negative consequences associated with work-related stress. This study evaluates the (cost-) effectiveness of two versions of an iSMI, minimal guided and unguided iSMI. Thus, the present study will further enhance the evidence-base for iSMI and provide valuable information about the optimal balance between outcome and economic costs.