Abstract Background Suicidal thoughts are common in the general population, causing significant disability. However, a substantial number of people struggling with suicidality do not access appropriate services. Online self-help may help overcome barriers to help-seeking. This study aims to examine the effectiveness of an online self-help program targeted at reducing suicidal thoughts compared with an attention-matched control condition in the Australian adult population. This trial is based on a Dutch self-help program, which was found to be effective in reducing suicidal thoughts. Methods/Design A total of 570 community-dwelling adults (18 to 65 years old) with suicidal thoughts will be recruited via various media and randomly assigned to the 6-week online program aimed at reducing suicidal thoughts or a 6-week attention-matched control program. Primary outcome measure is the severity of suicidal thoughts. Secondary outcome measures include suicide plans, capacity to cope with suicidal thoughts, reasons for living, symptoms of depression, hopelessness, anxiety/worry, rumination, panic, perceived burdensomeness and thwarted belongingness, acquired capability, alcohol consumption, insomnia, and various cost-effectiveness measures. Discussion Although the original Dutch trial found web-based self-help to be effective in reducing suicidal thoughts, randomized controlled trials (RCT) of online programs for suicidal thoughts are rare. The present study extends previous research by running the first English language RCT of this sort. As a result of the original study, the current RCT includes refinements to the design, including greater levels of participant anonymity and longer follow-up periods. Limitations of this trial include the potential for high drop-out and the inability to ascertain whether any suicides occur during the study. Trial registration Australian New Zealand Clinical Trials Registry (ANZCTR) Registration number: ACTRN12613000410752 (15 April 2013). Universal Trial Number (UTN): U1111-1141-6595 (15 April 2013).