Background Anemia is a prevalent public health concern in The Gambia and other developing nations. While previous studies relied on binary logistic regression, the Multinomial Survey Logistic Regression Model was developed to address complexities in survey design, including sampling weights, stratification, and clustering. Multiple Imputation with Chained Equations (MICE) was employed to address missing data in variables such as anemia level, contraceptive use, and malaria drug intake during pregnancy. Aim/Objective This study aims to determine the prevalence and factors of anemia among pregnant women across eight local government areas in The Gambia. The research focuses on Kanifing, Kuntaur, Mansakonko, Kerewan, Janjanbureh, Basse, Brikama, and Banjul. Given the limited research on anemia among pregnant women in The Gambia, there is a need for further investigation into this topic. Methods MICE were utilized to address missing data due to their validity in handling uncertainty. This method generates multiple reasonable datasets for imputation and analyzes them accurately. A survey logistic regression model was employed to assess data fitness, considering the complex sample design. Anemia levels were measured among 11,865 pregnant women aged 15 to 49 using a systematic questionnaire. The multinomial survey logistic regression model was utilized to account for sampling weights, stratification, and clustering, relaxing the premise of observation independence violated by conventional logistic regression. Results The study involved 11,865 expectant mothers, revealing mild, moderate, and severe cases of anemia with a prevalence of 44.6%. Factors associated with anemia included place of residence, local government area, contraceptive use, age, literacy level, and current pregnancy status. Conclusion Socio-economic, demographic, and environmental factors significantly impact anemia levels among reproductive women in The Gambia. Addressing factors such as place of residence, local government areas, contraceptive use, literacy level, and current pregnancy status is crucial in mitigating anemia risk. Government initiatives, such as improving access to sanitation facilities and offering free check-ups, could effectively address this public health concern.