Introduction Adequate intermittent preventive treatment (IPTp) uptake (≥3 doses) routinely delivered at antenatal clinics is effective in preventing malaria during pregnancy. Whereas, low IPTp uptake (24.0%) had been reported among pregnant women in Ebonyi State, there is paucity of studies comparing the uptake and its predictors in the urban and rural areas of Ebonyi State. We determined IPTp uptake and its predictors in the urban and rural areas of Ebonyi State. Methods We conducted a cross-sectional comparative study among 864 reproductive age women selected using multistage sampling. Using a structured interviewer-administered questionnaire, we collected data on respondent’s socio-demographic characteristics and IPTp uptake. Uptake was adjudged adequate if ≥3 doses were taken, otherwise inadequate. We estimated the proportion of women with adequate IPTp uptake and determined the factors associated with adequate uptake in rural and urban areas using chi square and multiple logistic regression at 5% level of significance. Results The mean ages of respondents in the urban and rural areas were 28.5±4.6 and 27.4±5.0 years respectively. Adequate IPTp uptake was 82.5% and 60.8% in the urban and rural respectively (p<0.001). In the urban area, women whose husbands had attained ≥ secondary education (aOR:2.9; 95%CI:1.2–7.4; p = 0.02) and those who paid for sulfadoxine/pyrimethamime (aOR:0.2; 95%CI: 0.1–0.6; p = 0.01) were 2.9 times more likely and 5 times less likely to take adequate IPTp respectively compared to respondents whose husbands had attained ≤ primary education and those who had sulfadoxine/pyrimethamine free. In the rural area, women who had attended ANC <4 times (aOR:0.4; 95%CI: 0.3–0.7; p<0.001) were 2.5 times less likely to take adequate IPTp compared to women that had attended ANC ≥4 times. Conclusion Uptake of IPTp was more in the urban than rural areas of Ebonyi State. Interventions that reinforce the importance of health professionals carrying out actions aimed at pregnant women and their partners (spousal) in order to guide them on preventive actions against malaria and other diseases are recommended in Ebonyi State.