World Health Organization/International Network of Rational use of Drugs (WHO/INRUD) indicators are widely used to assess medicine use. However, there is limited evidence on their validity in Namibia's primary health care (PHC) to assess the quality of prescribing. An analytical cross-sectional survey design was used to examine and validate WHO/INRUD indicators in out-patient units of two PHC facilities and one hospital in Namibia from 1 February 2015 to 31 July 2015. Out of 1243 prescriptions; compliance to NSTG prescribing in ambulatory care was sub-optimal (target was >80%). Three of the four WHO/INRUD indicators did not meet Namibian or WHO targets: antibiotic prescribing, average number of medicines per prescription and generic prescribing. The majority of the indicators had low sensitivity and/or specificity. All WHO/INRUD indicators had poor accuracy in predicting rational prescribing.