Background Intermittent Preventive Treatment of malaria in infants (IPTi) is a malaria control strategy consisting of the administration of an anti-malarial drug alongside routine immunizations. So far, this is being implemented nationwide in Sierra Leone only. IPTi has been renamed as Perennial Malaria Chemoprevention -PMC-, accounting for its recently recommended expansion into the second year of life. Before starting a pilot implementation on PMC, the currently implemented strategy and malaria prevalence were assessed in young children in selected areas of Sierra Leone. Methods A cross-sectional, community-based, multi-stage cluster household survey was conducted from November to December 2021 in selected districts of the Northern and northwestern provinces of Sierra Leone among 10–23 months old children, whose caretakers gave written informed consent to participate in the survey. Coverage of IPTi and malaria prevalence—assessed with rapid diagnostic tests—were calculated using percentages and 95% confidence intervals weighted for the sampling design and adjusted for non-response within clusters. Factors associated with RDT + and iPTi coverage were also assessed. Results A total of 720 children were recruited. Coverage of three IPTi doses was 50.57% (368/707; 95% CI 45.38–55.75), while prevalence of malaria infection was 28.19% (95% CI 24.81–31.84). Most children had received IPTi1 (80.26%, 574/707; 95% CI 75.30–84.44), and IPTi2 (80.09%, 577/707; 95% CI 76.30–83.40) and over half of the children also received IPTi3 (57.72%, 420/707; 95% CI 53.20–62.11). The uptake of each IPTi dose was lower than that of the vaccines administered at the same timepoint at all contacts. Conclusion In Sierra Leone, half of the children received the three recommended doses of IPTi indicating an increase in its uptake compared to previous data of just a third of children receiving the intervention. However, efforts need to be made in improving IPTi coverage, especially in the planned expansion of the strategy into the second year of life following recent WHO guidelines.