Background: Parental well-being can be seriously impacted during the challenging perinatal period. Most research and support services focus on perinatal psychopathology, leaving a need for programs that recognize and enhance the strengths and well-being of parents. Furthermore, fathers have received minimal attention and support relative to mothers, despite experiencing perinatal distress. New parents have limited time and energy to invest in program attendance, and web-based programs provide an ideal platform for delivering perinatal well-being programs. Such programs are globally accessible, available at any time, and can be accessed anywhere with an Internet connection. Objective: This paper describes the protocol of a randomized controlled trial investigating the effects on first-time parents’ perinatal well-being, comparing two versions of the online program Baby Steps. Methods: The clinical trial will randomize 240 primiparous mother-father couples to either (1) Babycare, an online information-only program providing tips on selected childcare issues, or (2) Well-being, an online interactive program including all content from the Babycare program, plus parental well-being-focused content with tools for goal-setting and problem solving. Both programs will be supported by short message service (SMS) texts at two, four, seven, and ten weeks to encourage continued use of the program. Primary outcomes will be measures of perinatal distress and quality of life. Secondary outcomes will be couple relationship satisfaction, parent self-efficacy, and social support. Cost-effectiveness will also be measured for each Baby Steps program. Results: Participant recruitment commenced March, 2015 and continued until October, 2015. Follow-up data collection has commenced and will be completed May, 2016 with results expected in July, 2016. Conclusions: Perinatal distress has substantial impacts on parents and their infants, with potential to affect later childhood adjustment, relationships, and development. This study aims to test the impact of a highly accessible online program to support parental coping, and maximize the well-being of both parents. By including fathers in the program, Baby Steps has the potential to engage and support this often neglected group who can make a substantial contribution to familial well-being.