Even though antiretroviral therapy (ART) access for human immunodeficiency virus (HIV)-infected children increased dramatically, anaemia has continued as a challenge regardless of a cluster of differentiation (CD4) count and viral load. Hence, the present study aimed to assess the determinants of iron deficiency anaemia among children living with HIV after the initiation of ART. An institution-based unmatched case–control study was conducted among consecutively selected 712 children on HIV care from 1 September to 30 October 2022 in the Metekel zone. A pre-tested and structured data extraction checklist was used to collect the data. Data were analysed using STATA version 16 software. Binary logistic regression was used to find the association between independent variables and anaemia. The level of statistical significance was declared at a value of P < 0⋅05. A total of 712 HIV-positive children (178 cases and 534 controls) were included in this study, with a completeness rate of 98⋅8 %. In multivariable analysis, variables that have a statistically significant association with anaemia were as follows: CD4 count <350 (Adjusted Odds Ratio [AOR] 2⋅76; 95 % CI 1⋅76, 4⋅34), World Health Organization (WHO) clinical stage III (AOR 7⋅9; 95 % CI 3⋅5, 17⋅91) and stage IV (AOR 7⋅8; 95 % CI 3⋅37, 18⋅1), cotrimoxazole prophylaxis therapy (AOR 0⋅5; 95 % CI 0⋅31, 0⋅8) and mid-upper arm circumference (MUAC) ≤11⋅5 mm (AOR 2⋅1; 95 % CI 1⋅34, 3⋅28). The present study found that CD4 count, WHO clinical stage, cotrimoxazole prophylaxis therapy and MUAC were significantly associated with anaemia in children on ART. Therefore, continuous screening of anaemia and nutritional treatment is essential in these patients.