Objective To identify areas of deficiencies and gaps in child protection services in Northern Sri Lanka. Also, to help in recommending strategies, programmes of interventions for addressing issues of child abuse and advice the legal system. Methods A retrospective study was done to determine the socio-demographic details, type of abuse, clinical profile, relationship of the perpetrator and nature of abuse among children admitted to a tertiary care centre from 2009 through 2014, a period after cessation of a 60-y conflict. Data were obtained from hospital based records and records maintained at the district probation office. Results Seven hundred twenty cases were referred to the tertiary care centre with abuse. Majority of the children were from the Jaffna district, the northern city of the war affected area and mean age of the children affected was 14.5 +/- 2.6 y. Females were affected more than the males and 352 children were seen following sexual abuse. The clinical examination showed penetrative injury in 15 %. The perpetrator was known in 70 % of the situations and the victim was coerced into a relationship for abuse. Attempted suicide was seen in significant numbers during the immediate post war period and school dropout and delinquent behaviour was seen in later years. Conclusions The problem of child abuse is considerable in this region and there is an urgent need to strengthen the services offered to the victims. Urgent steps are needed to safeguard these children, especially in the war affected areas.