Background: The National Essential Medicine System (NEMS) is a new policy in China launched in 2009 to improve the appropriate use of medications. This study aims to examine the outcomes of the NEMS objectives in terms of the rational use of medicines in primary health care facilities in China. Methods: A total of 28,651 prescriptions were collected from 146 township health centers in four provinces of China by means of a field survey conducted in 2010-2011. Indicators of rational drug use were extracted and compared using a pre/post design and then evaluated with regard to the World Health Organization (WHO) Standard Guidelines and data from previous research. Results: The average number of drugs per prescription decreased from 3.64 to 3.46 (p < 0.01) between 2009 and 2010. Little effect was found for the NEMS on the average number of antibiotics per prescription, but the percentage of prescriptions including antibiotics decreased from 60.26 to 58.48% (p < 0.01). Prescriptions for injections or adrenal corticosteroids also decreased, to 40.31 and 11.16% of all prescriptions, respectively. All these positive issues were also recorded in 2011. However, each of the above values remained higher than WHO standards. The percentage of drugs prescribed from the Essential Drug List increased after the implementation of the NEMS (p < 0.01). Where the available data allowed changes in costs to be assessed, the average expense per prescription increased significantly, from 25.77 to 27.09 yuan (p < 0.01). Conclusions: The NEMS effectively improved rational medicine use in China. However, polypharmacy and the overprescription of antibiotics and injections remain common. There is still a large unfinished agenda requiring policy improvements. Treatment guidelines, intensive support supervision, and continuing training for both professionals and consumers are the essential actions that need to be taken. © 2014 Song et al.; licensee BioMed Central Ltd.