Low birth weight prevalence in Malaysia remains high. Socioeconomic background may lead to differences in physical activity and maternal nutritional status, which may play an important role in birth outcomes. This prospective cross-sectional study aimed to identify rural-urban differences in risk factors for low birth weight among women in Malaysia. Pregnant women at ≥20 weeks of gestation in urban and rural Malaysia (n = 437) completed questionnaires on sociodemographic characteristics and physical activity. Weight and middle-upper arm circumference were measured. Infant birth outcomes were extracted from medical records. The overall prevalence of low birth weight infants was 6.38%. Rural women had more low birth weight infants than urban women (9.8% vs 2.0%, p = 0.03). Findings showed rural women were less sedentary (p = 0.003) and participated in more household/caregiving activities (p = 0.036), sports activities (p = 0.01) and less occupational activity (p < 0.001) than urban women. Logistic regression revealed that older age (OR = 1.395, 95% Cl = 1.053 to 1.846), low parity (OR = 0.256, 95% Cl = 0.088-0.747) and low middle-upper arm circumference (OR = 0.738, 95% Cl = 0.552 to 0.987) increased the risk of low birth weight infants in rural, but not in urban women. We observed differences in risk factors for low birth weight between urban and rural pregnant women. Age, malnutrition and low parity were risk factors for low birth weight among rural pregnant women. Our findings suggest that rural pregnant women with low nutritional status should be encouraged to monitor their middle-upper arm circumference consistently throughout pregnancy. Improving nutritional status in rural pregnant women may reduce the risk of low birth weight infants in this population.