BACKGROUND: There is limited literature regarding adherence rates for the treatment of tuberculosis (TB) in children. We aimed to describe TB treatment outcomes and adherence as well as to evaluate associated factors to poor adherence in Mozambican children. METHODS: This is a sub-study of a community TB incidence study among children <3 years of age. Incomplete adherence included the sum of lost-to-follow-up cases plus those with a delay of > 3 weeks to treatment completion. RESULTS: Fifty TB treatments were assessed. Forty-four (88.0%) patients completed treatment, two (4.0%) died during treatment and four (8.0%) were lost to follow-up. Incomplete adherence was observed in 31.3% (15 of 48) of cases and was associated with malnutrition or history of a migrant mother. CONCLUSION: Although treatment outcome is overall good, there is still a significant proportion of incomplete adherence. Further larger paediatric TB cohorts and qualitative approaches are needed to assess and confirm potential factors for non-adherence.