Background: The prevalence of malaria in pregnancy and its complications, remain very high in Nigeria. This study aimed to determine the effects of a malaria health educational intervention based on the information-motivation-behavioural skills (IMB) model on malaria preventive practices and pregnancy outcomes. Methods: The study was a randomized controlled parallel-group study, where 372 randomly selected antenatal care attendees were randomly assigned to one of either two groups after collecting baseline data. The intervention group then received a four-hour health education intervention developed based on the IMB model, while the control group received a similarly designed health education on breastfeeding, and were then followed-up to the end of their pregnancies. The intention-to-treat analysis using the generalized linear mixed models was used to analyse the data obtained. Results: The reported frequency of ITN use and dose of IPTp taken, were higher in the intervention group by 0.32 levels (p=0.024) and 0.37 doses (p<0.001) respectively, implying that for 32% and 37% of the participants, an individual in the intervention group slept more frequently under an ITN by one day, and had also took one dose of IPTp more than an individual in the control group. The intervention group also achieved a haematocrit level of 0.80% higher than the control group. The intervention however, had no significant effect on the incidence of malaria diagnosis or babies’ birth weights. Conclusion: The intervention was effective in improving ITN use, IPTp uptake, and haematocrit levels. It is therefore recommended for the module to be adopted and incorporated into the routine antenatal care programmes in the state. Trial registration: Pan African Clinical Trial Registry, PACTR201610001823405. Registered 26 October 2016, www.pactr.org.