Background: Artemisinin-based combination treatments (ACTs) are the recommended first-line antimalarials globally, but their influence on the risk factors associated with gametocyte carriage has had little evaluation in endemic areas. Methods: The risk factors associated with gametocytaemia at presentation and after ACTs were evaluated in 835 children assigned to artesunate, artesunate-amodiaquine, artesunate-mefloquine or artemether-lumefantrine. Results: Gametocyte carriage at enrolment was 8.4%. During follow-up, 24 patients (2.8%) developed gametocytaemia, which in 83% (20 patients) had developed by day 7 following treatment. In a multiple regression model, 2 factors were independent risk factors for the presence of gametocytaemia at enrolment, namely age <3 years (adjusted odds ratio 2.03, 95% confidence interval 1.01–4.05; p = 0.04) and enrolment before 2009 (adjusted odds ratio 4.2, 95% confidence interval 2.09–8.44; p < 0.001). Haematocrit <25% and parasitaemia <50,000/µl blood were associated with an increased risk of gametocytaemia. Following treatment, 3 factors were independent risk factors for gametocytaemia, namely gametocytaemia at enrolment (adjusted odds ratio 46.39, 95% confidence interval 22.3–96.46; p < 0.0001) and treatment with artesunate (adjusted odds ratio 6.74, 95% confidence interval 1.79–25.27; p = 0.005) or artesunate-mefloquine (adjusted odds ratio 9.66, 95% confidence interval 2.87–32.46; p < 0.0.0001) relative to other ACTs. Conclusion: ACTs modified the risk factors associated with gametocyte carriage after use.