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Background: Although Nigeria has made some progress in malaria control, there are variations across States. We investigated the factors associated with utilisation of long-lasting insecticide-treated net (LLIN) and parasitaemia among under-five children in 13 States with high malaria burden. Method: Data from the 2015 Nigeria Malaria Indicator Survey and 2018 Demographic and Health Survey were obtained and analysed. The 2015 and 2018 data were compared to identify States with increase or reduction in parasitaemia. Analysis was done for all the 13 study States; four States with increased parasitaemia and nine States with reduction. Random-effects logit models were fitted to identify independent predictors of LLIN utilisation and parasitaemia. Results: LLIN was used by 53.4% of 2844 children, while parasitaemia prevalence was 26.4% in 2018. Grandchildren (AOR = 5.35, CI: 1.09–26.19) were more likely to use LLIN while other relatives (AOR = 0.33, CI: 0.11–0.94) were less likely compared to children of household-heads. LLIN use was more common in children whose mother opined that only weak children could die from malaria (AOR = 1.83, CI: 1.10–3.10). Children whose mothers obtained net from antenatal or immunisation clinics (AOR = 5.30, CI: 2.32–12.14) and campaigns (AOR = 1.77, CI: 1.03–3.04) were also more likely to use LLIN. In contrast, LLIN utilisation was less likely among children in female-headed households (AOR = 0.51, CI: 0.27–0.99) and those in poor-quality houses (AOR = 0.25, CI: 0.09–0.72). Children aged 24–59 months compared to 0–11 months (AOR = 1.78, CI: 1.28–2.48), those in whom fever was reported (AOR = 1.31, CI: 1.06–1.63) and children of uneducated women (AOR = 1.89, CI: 1.32–2.70) were more likely to have parasitaemia. The likelihood of parasitaemia was higher among children from poor households compared to the rich (AOR = 2.06, CI: 1.24–3.42). The odds of parasitaemia were 98% higher among rural children (AOR = 1.98, CI: 1.37–2.87). Conclusion: The key drivers of LLIN utilisation were source of net and socioeconomic characteristics. The latter was also a key factor associated with parasitaemia. These should be targeted as part of integrated malaria elimination efforts. [ABSTRACT FROM AUTHOR]