Objective: To assess the haematological profile of children with malaria, treated with three different artemisinin-based combination therapies in South Eastern Nigeria. Methods: Using a multistage sampling technique, blood samples were collected from 105 randomly selected malaria positive primary school children aged 6-13 years. Pre- and post-assessment of their haematological profiles were respectively done on intervention of three different artemisinin-based combination therapies. Results: Result showed a strong difference [(0.38 ± 0.31) g/dL] in haemoglobin levels with the artesunate-amodiaquine (t = 7.30, P < 0.05). Dihydroartemisinin-piperaquine (DP) and artemether-lumefantrine showed haemoglobin (t = 4.49, P < 0.05) with mean difference [(0.64 ± 0.85) g/dL] and (t = 6.09, P < 0.05) with mean difference [(0.80 ± 0.78) g/dL] respectively. The mean difference of white blood cell was found to be negative but significant with artesunate-amodiaquine (-1.07 ± 3.12) at 95% confidence intervel (CI) (-2.14, 0.00) and artemether-lumefantrine (-0.36 ± 0.28) at 95% CI (-0.45, -0.26) interventions respectively. Significant mean difference of neutrophils was only found for the DP interventions (4.54 ± 8.30) at 95% CI (1.69, 7.40) while lymphocytes indicated a significant mean difference between the pre/post-interventions (-3.60 ± 9.34) at 95% CI (-6.81, -0.39) with DP only. Conclusions: Even though these findings do not indicate any life threatening events, they may have some useful implications for investigating future non-infectious diseases of blood origin. Further studies to determine the extent of involvement of malaria parasite as well as drug interactions in haematological alterations vis-a-vis its implication for noncommunicable disease are important.