Background: Malnutrition is appreciated as a global leading paediatric burden that indirectly or directly contributes to child mortality. In children, malnutrition has profound effects on health and development; and has been associated with poor outcomes in paediatric diseases. However, it is not clear if malnourished children are at an increased risk of having malaria. This study was conducted to evaluate the risk of malaria infection in children with malnutrition. Methods: The study design was pre-post. A protective clothing against mosquitoes (pCAM) was given to 102 underfive children in two coastal communities, after screening for malaria parasitaemia. The children's weight, height and body temperature were measured at recruitment. Blood was also taken at recruitment and monthly for malaria parasitaemia, haemoglobin concentration and random blood sugar. The parents/care-givers were visited daily for 1 month only, after recruitment, to ensure that the children wore the pCAM daily from 5 pm and the children were followed up monthly for 2 months. Results: Of the 102 study participants, 60 (24 males and 36 females) were rapid diagnostic test (RDT)-positive at recruitment, indicating 58.8% prevalence of malaria parasitaemia. The prevalence of malnutrition and of stunting were 32.3% (33/102) and 54.9% (56/102), respectively, while 7.8% (8/108) children were wasted. Twenty (60.6%) of the malnourished children and 30 (53.6%) of those stunted were RDT-positive at recruitment. At the first post-intervention screening, only 7 (31.8%) of the malnourished and 13 (28.9%) of those stunted were RDT-positive. Malnourished and stunted children were 2.57 times and 2.31 times more likely to be malaria infected (OR = 2.57, 95% CI 0.97, 6.79; OR = 2.31, 95% CI 1.01, 5.26 respectively). Malnourished females were 2.72 times more likely to be RDT-positive compared to malnourished males (OR = 2.72, 95% CI 0.54, 11.61) and stunted females were 1.73 times more likely to the positive for malaria parasites than stunted males (OR 1.73, 95% CI 0.59, 5.03). The prevalence of anaemia at recruitment decreased from 82.4 to 69.6% after intervention. The mean haemoglobin concentration (g/dl) at recruitment was significantly lower (P < 0.05) than that at 1st and 2nd post-intervention measurements (9.6 ± 1.4, t = − 3.17,