Introduction Primary care services are essential in achieving universal health coverage and Malaysia is looking into public-private partnership to overcome resource constraints. The study aims to compare the performance of primary care service delivery dimensions between public and private sector. Methods This cross-sectional study used the data from the Malaysian International Quality and Costs of Primary Care (QUALICOPC) study conducted in 2015–2016. The relative performance of each sector in four dimensions was compared using multi-level linear regression by incorporating a dummy variable indicating public sector in the model. Results The public sector was shown to have higher performance in comprehensiveness and coordination, while the private sector was better in continuity. There was no significant difference in accessibility. The public primary care services were better in serving primary care sensitive conditions, better informational continuity, and with better skill-mix and inter- and intra- professional relationship. Meanwhile, the private sector was stronger in referral decision making process, specialist feedback and greater out of hours facilities access. Conclusions The public and private sectors differ in their strengths, which the government may tap into to strengthen primary care services. Other areas for improvement include seamless care strategies that promote good referral, feedback, and information continuity.