Background: Child abuse and postnatal depression are two public health problems that often co-occur, with rates of childhood maltreatment highest during the first year of life. Internet-based behavioural activation (iBA) therapy has demonstrated its efficacy for improving postnatal depression. No study has examined whether the iBA program is also effective at preventing child abuse. This study aims to investigate whether iBA improves depressive symptoms among mothers and prevents abusive behaviours towards children in postpartum mothers in a randomized controlled trial, stratifying on depressive mood status. The study also evaluates the implementation aspects of the program, including how users, medical providers, and managers perceive the program in terms of acceptability, appropriateness, feasibility, and harm done. Methods: The study is a non-blinded, stratified randomized controlled trial. Based on cut-off scores validated on Japanese mothers, participants will be stratified to either a low Edinburgh Postnatal Depression Scale (EPDS) group, (EPDS 0–8 points) or a high EPDS group (EPDS ≥9 points). A total of 390 postnatal women, 20 years or older, who have given birth within 10 weeks and have regular internet-access will be recruited at two hospitals. Participants will be randomly assigned to either treatment, with treatment as usual (TAU) or through intervention groups. The TAU group receives 12 weekly iBA sessions with online assignments and feedback from trained therapists. Co-primary outcomes are maternal depressive symptoms (EPDS) and psychological aggression toward children (Conflict Tactic Scale 1) at the 24-week follow-up survey. Secondary outcomes include maternal depressive symptoms, parental stress, bonding relationship, quality of life, maternal health care use, and paediatric outcomes such as physical development, preventive care attendance, and health care use. The study will also investigate the implementation outcomes of the program. Discussion: The study investigates the effectiveness of the iBA program for maternal depressive symptoms and psychological aggression toward children, as well as implementation outcomes, in a randomized-controlled trial. The iBA may be a potential strategy for improving maternal postnatal depression and preventing child abuse. Trial registration: The study protocol (issue date: 2019-Mar-01, original version 2019005NI-00) was registered at the UMIN Clinical Trial Registry (UMIN-CTR: ID UMIN 000036864).