Paternal perinatal mental health significantly impacts family outcomes, yet fathers are often overlooked and underserved in mental health services. This study evaluates the efficacy of a mindfulness-based cognitive behaviour therapy intervention delivered via mobile app to address paternal perinatal depression, anxiety, and stress symptoms. A randomised controlled trial was conducted with perinatal fathers experiencing moderate depression, anxiety, or stress symptoms. Participants were assigned to either the Rover app mindfulness-based CBT intervention (n = 81) or an active control app, moodmonitor (n = 75). Primary outcomes were depression (EPDS), anxiety, and stress (DASS21); secondary outcomes included social support, parenting self-efficacy, and couple relationship quality. Post-test analysis occurred at four weeks, with an additional eight-week follow-up for the intervention group. Contrary to hypotheses, no differences were found between groups for depression, anxiety, and stress symptoms. Both groups showed significant reductions in anxiety (intervention d = -1.7, control d = -1.94) and stress (intervention d = -2.9, control d = -2.8) and improved couple relationship quality. Rover users maintained improvements at 8-week follow-up. Fathers with severe baseline depression experienced greater reductions in depression using the Rover app (b = 5.36, p < 0.01). Low adherence to the intervention and moderate attrition over the study duration. Although the intervention was acceptable to fathers, treatment adherence was low, highlighting the need for more engaging content. App-based interventions show potential benefits for paternal mental health, but user engagement must be improved. This study contributes to the growing literature on digital interventions for fathers' mental health and emphasizes the importance of including fathers in perinatal mental health research. Australian and New Zealand Clinical Trials Registry: ACTRN12621000275864.