Background Tuberculosis (TB) is a leading cause of death in children and adults. Unlike for adults, there is paucity of data on childhood TB in several countries in Africa. The study objective was to assess the characteristics and treatment outcomes of children with TB from multiple health facilities in Accra, Ghana. Methods A retrospective analyses was conducted using secondary data on children less than 15 years collected from 11 facilities during a TB case finding initiative in Accra from June 2010 to December 2013. Demographic and clinical characteristics as well as treatment outcomes were assessed. Multivariable logistic regression was conducted to assess predictors of mortality. Results Out of the total 3704 TB cases reported, 5.9% (219) consisted of children with a female: male ratio of 1:1.1. Children less than 5 years made up 56.2% of the patients while 44.2% were HIV positive. The distribution of TB type were as follows: smear positive pulmonary TB (SPPTB), 46.5%, clinically diagnosed pulmonary TB 36.4%.%, extra-pulmonary TB 17.4%. Among the 214 children (97.7%) for whom treatment outcome was documented, 194 (90.7%) were successfully treated consisting of 81.3% who completed treatment and 9.4% who were cured. Eighteen children (8.4%) died. Mortality was significantly higher among the 1–4 year group ( p < 0.001), those with SPPTB (p < 0.001) and HIV positive children (p < 0.001). In logistic regression, SPPTB and HIV positivity were predictors of mortality. Conclusion The proportion of children in Accra successfully treated for TB met the target of END TB Strategy treatment success indicator. HIV positivity was a risk factor for death. Reducing mortality in TB-HIV co-infected children will further improve treatment outcomes of children with TB in Accra.