In Malaysia, first-contact, primary care is provided by parallel public and private sectors, which are completely separate in organization, financing and governance. As the country considers new approaches to financing, including using public schemes to pay for private care, it is crucial to examine the quality of clinical care in the two sectors to make informed decisions on public policy. This study intends to measure and compare the quality of clinical care between public and private primary care services in Malaysia and, to the extent possible, assess quality with the developed economies that Malaysia aspires to join. We carried out a retrospective analysis of the National Medical Care Survey 2014, a nationally representative survey of doctor-patient encounters in Malaysia. We assessed clinical quality for 27 587 patient encounters using data on 66 internationally validated quality indicators. Aggregate scores were constructed, and comparisons made between the public and private sectors. Overall, patients received the recommended care just over half the time (56.5%). The public sector performed better than the private sector, especially in the treatment of acute conditions, chronic conditions and in prescribing practices. Both sectors performed poorly in the indicators that are most resource intensive, suggesting that resource constraints limit overall quality. A comparison with 2003 data from the USA, suggests that performance in Malaysia was similar to that a decade earlier in the USA for common indicators. The public sector showed better performance in clinical care than the private sector, contrary to common perceptions in Malaysia and despite providing worse consumer quality. The overall quality of outpatient clinical care in Malaysia appears comparable to other developed countries, yet there are gaps in quality, such as in the management of hypertension, which should be tackled to improve overall health outcomes.