Introduction Research using routinely collected primary health care data can improve health care quality, outcomes, policy, and health equity. Aotearoa New Zealand (NZ) lacked the infrastructure to readily access these data. The Southern Primary Care Research Network (Southern PCRN) has been established to address this issue.Aim This study aimed to identify the research priorities of primary health care clinicians and researchers.Methods A modified Delphi survey method was used to identify priority general research areas and specific research questions in NZ primary health care. Participants suggested priority research areas and research questions in Round 1. These were grouped thematically and ranked by frequency. Research questions were screened by scope and feasibility. In Round 2, participants ranked the importance of the research questions.Results Primary health care access, health workforce, health services, mental health, and models of primary health care were identified as priority research areas. After screening, 23 research questions were included in Round 2. Consensus was reached on 20 questions. The highest-ranked questions suggested implementation and evaluation of annual checks for people with intellectual disability, and evaluating the effects of embedding allied health practitioners and social workers in primary health care teams.Discussion Prioritised research areas are consistent with those identified in the literature. However, the priority research questions are emerging topics. This is the first research prioritisation exercise undertaken for the Southern PCRN. Further research is planned to explore patient priorities. These findings will help the Southern PCRN to establish a research agenda in accordance with its mission of improving health equity. What is known about the topic: Routinely collected administrative and health data have potential to be used for research that provides real-world health insights that can inform policy and improve clinical practice and population health. Engaging stakeholders to establish priorities can help ensure research is fit for purpose, provides important health benefits, and has the greatest potential to improve health equity. What this study adds: Primary care clinicians and academics identified the top research areas to improve health equity in primary care as the health workforce, health services, mental health, and models of primary health care. The top research questions include evaluating the impacts of annual health checks for people with intellectual disability, the role of allied health as front-line primary health care providers, and the role of an embedded social worker in a general practice clinic setting.