Background: A considerable percentage of flight crew reports to be fatigued regularly. This is partly caused by irregular and long working hours and the crossing of time zones. It has been shown that persistent fatigue can lead to health problems, impaired performance during work, and a decreased work-private life balance. It is hypothesized that an intervention consisting of tailored advice regarding exposure to daylight, optimising sleep, physical activity, and nutrition will lead to a reduction of fatigue in airline pilots compared to a control group, which receives a minimal intervention with standard available information. Methods/design. The study population will consist of pilots of a large airline company. All pilots who posses a smartphone or tablet, and who are not on sick leave for more than four weeks at the moment of recruitment, will be eligible for participation.In a two-armed randomised controlled trial, participants will be allocated to an intervention group that will receive the tailored advice to optimise exposure to daylight, sleep, physical activity and nutrition, and a control group that will receive standard available information. The intervention will be applied using a smartphone application and a website, and will be tailored on flight- and participant-specific characteristics. The primary outcome of the study is perceived fatigue. Secondary outcomes are need for recovery, duration and quality of sleep, dietary and physical activity behaviours, work-private life balance, general health, and sickness absence. A process evaluation will be conducted as well. Outcomes will be measured at baseline and at three and six months after baseline. Discussion. This paper describes the development of an intervention for airline pilots, consisting of tailored advice (on exposure to daylight and sleep-, physical activity, and nutrition) applied into a smartphone application. Further, the paper describes the design of the randomised controlled trial evaluating the effect of the intervention on fatigue, health and sickness absence. If proven effective, the intervention can be applied as a new and practical tool in fatigue management. Results are expected at the end of 2013. Trial registration. Netherlands Trial Register: NTR2722. © 2013 van Drongelen et al.; licensee BioMed Central Ltd.