Abstract Background With increasing access to effective Anti-Retroviral Therapy (ART), the proportion of children who survive into later childhood with HIV has increased. Consequently, caregivers are constantly being confronted with the dilemma of ‘if’, ‘when’, and ‘how’ to tell their children living with HIV their status. We aimed to determine the prevalence and predictors of disclosure and explore the barriers caregivers face in disclosing HIV status to children living with HIV in Gombe, northeast Nigeria. Methods We conducted a sequential, explanatory, mixed-methods study at the specialist Paediatric HIV clinic of the Federal Teaching Hospital Gombe, northeast Nigeria. The quantitative component was a cross sectional, questionnaire-based study that consecutively recruited 120 eligible primary caregivers of children (6–17 years) living with HIV. The qualitative component adopted an in-depth one-on-one interview approach with 17 primary caregivers. Primary caregivers were purposively selected to include views of those who had made disclosure and those who have not done so to gain an enhanced understanding of the quantitative findings. We examined the predictors of HIV status disclosure to infected children using binary logistic regression. The qualitative data was analysed using a combined deductive and inductive thematic analysis approach. Results The mean age of the index child living with HIV was 12.2 ± 3.2 years. The prevalence of disclosure to children living with HIV was 35.8%. Children living with HIV were 10 times more likely to have been told their status if their caregivers believed that disclosure had benefits [AOR = 9.9 (95% CI = 3.2–15.1)], while HIV-negative compared to HIV-positive caregivers were twice more likely to make disclosures [AOR = 1.8 (95%CI = 0.7–4.9)]. Girls were 1.45 times more likely than boys to have been disclosed their HIV positive status even after adjusting for other variables [AOR = 1.45 (95% CI = 0.6–3.5)]. Caregivers expressed deep-seated feeling of guilt and self-blame, HIV-related stigma, cultural sensitivity around HIV, and fears that the child might not cope as barriers to non-disclosure. These feeling were more prominent among HIV-positive caregivers. Conclusion The process of disclosure is a complex one and caregivers of HIV positive children should be supported emotionally and psychologically to facilitate disclosure of HIV status to their children. This study further emphasises the need to address HIV-related stigma in resource constrained settings.