Although the detrimental impact of child sexual abuse is well documented, there is a dearth of literature on differential outcomes and on child protection services by gender. Using a representative dataset of child welfare investigations, this paper explores how boys and girls investigated by the child protection system for alleged sexual abuse (n = 4,261) compare on key clinical characteristics and on the likelihood of a transfer to ongoing services. These characteristics include sexual abuse type, associated physical and emotional harm, and caregiver and child functioning concerns. The results indicate that there are significant differences in child functioning concerns by gender, with investigations involving boys having a stronger association with aggressive behaviour, attention problems, academic difficulties, depression, and the presence of an intellectual disability. Paradoxically, although sexual abuse investigations involving boys are less likely to note emotional harm and be substantiated, they are more likely to be transferred to ongoing child welfare services.