BackgroundMalaria is the main cause of hospital admissions in Benin and a leading cause of death in childhood. Beside consultations, various studies have underlined the management of the disease through home treatment. The medicines used can be purchased in informal market of pharmaceutical drugs (IMPD) without prescription or any involvement of healthcare professional. Pharmaceutical drugs are sold by informal private vendors, who operate at any time in the immediate environment of the patients. The present study was conducted in Cotonou to study the health-seeking behaviour of caregivers to treat malaria in children under 12 years old. Factors associated with malaria home treatment and drugs purchase in IMPD were studied.MethodsA cross-sectional study was carried out among 340 children’s caregivers who were interviewed about their socio-demographic characteristics and their care-seeking behaviour during the most recent episode of malaria in their children under 12. Medicines used and purchase place were also collected. Multivariate logistic regression model was used to determine factors associated with malaria home treatment and drug purchase in IMPD.ResultsBeyond all the 340 caregivers, 116 (34%) consulted healthcare professional, 224 (66%) home treat the children, among whom 207 (61%) gave pharmaceutical drugs and 17 (5%) gave traditional remedies to children. Malaria home treatment was associated with family size, health insurance (OR = 0.396, 95% CI 0.169–0.928), and wealth quintiles where home treatment was less used by the richest (OR = 0.199, 95% CI 0.0676–0.522) compared to those in the poorest quintile. The caregivers age group 30–39 years was associated to the use of IMPD (OR = 0.383, 95% CI 0.152–0.964), the most economically wealthy people were less likely to use IMPD (wealth quintile richest: OR = 0.239, 95% CI 0.064–0.887; wealth quintile fourth OR = 0.271, 95% CI 0.100–0.735) compared to those in the poorest quintile. All caregivers who benefited from health insurance did not use IMPD.ConclusionThis study highlights the link between worse economic conditions and accessibility to medical care as one of the main factors of malaria home treatment and drug purchase in IMPD, even if those two phenomena need to be understood apart.Electronic supplementary materialThe online version of this article (10.1186/s12936-018-2504-1) contains supplementary material, which is available to authorized users.