To assess the impact of the National Essential Medicines Scheme (NEMS) with respect to urban-rural inequalities regarding drug prescriptions in primary care facilities.A stratified two-stage random sampling strategy was used to sample 23,040 prescriptions from 192 primary care facilities from 2009 to 2010. Difference-in-Difference (DID) analyses were performed to test the association between NEMS and urban-rural gaps in prescription patterns. Between-Group Variance and Theil Index were calculated to measure urban-rural absolute and relative disparities in drug prescriptions.The use of the Essential Medicines List (EML) achieved a compliance rate of up to 90% in both urban and rural facilities. An overall reduction of average prescription cost improved economic access to drugs for patients in both areas. However, we observed an increased urban-rural disparity in average expenditure per prescription. The rate of antibiotics and glucocorticoids prescription remained high, despite a reduced disparity between urban and rural facilities. The average incidence of antibiotic prescription increased slightly in urban facilities (62 to 63%) and reduced in rural facilities (67% to 66%). The urban-rural disparity in the use of parenteral administration (injections and infusions) increased, albeit at a high level in both areas (44%-52%).NEMS interventions are effective in reducing the overall average prescription costs. Despite the increased use of the EML, indicator performances with respect to rational drug prescribing and use remain poor and exceed the WHO/INRUD recommended cutoff values and worldwide benchmarks. There is an increased gap between urban and rural areas in the use of parenteral administration and expenditure per prescription.