Objectives HealthPathways, pioneered in Canterbury, New Zealand, in 2008, is a web-based tool designed to promote health care integration and patient management in primary care and to reduce fragmentation in the delivery of health services. This cross-sectional study evaluated the utilisation and perceptions of this tool among health professionals in Australia and New Zealand. Methods A cross-sectional survey was administered online through Research Electronic Data Capture (REDCap) to general practitioners (GPs), practice nurses and managers, nurse practitioners, specialist and community nurses, hospital clinicians, nurses, managers, and allied health professionals between April and September 2018. The frequency of HealthPathways use in the previous month was modelled as an ordered response using an ordered logistic regression model after adjusting for the possible effects of sex, age, years in clinical practice, location and time spent in practice. Results Health professionals perceived HealthPathways to be useful in primary care management and referral, as well as in the prereferral treatment of patients. GPs in New Zealand, New South Wales and Victoria were 73%, 47% and 27% more likely to have used HealthPathways ≥10 times in the previous month respectively. Conclusion The results suggest that HealthPathways is having a positive effect on healthcare systems in New Zealand and Australia. However, differences in uptake suggests the need for focused implementation, integration into eReferral software and expanding the tool to medical students, registrars, allied health professionals and potentially patients to encourage behavioural change. What is known about the topic? Early evaluations suggest that HealthPathways is a useful tool for health professionals, although uptake and utilisation may be limited. However, there is no comparative evidence regarding uptake and implementation of the tool. What does the paper add? This study is among the first to provide a comparative narrative of the literature assessing the implementation and uptake of HealthPathways across Australia and New Zealand. It is also among the first to compare the perceptions of allied health professionals in the use of HealthPathways across Australia and New Zealand. What are the implications for practitioners? The results of this study suggest the need for focused implementation, integration into eReferral software and expanding the tool to medical students, registrars, allied health professionals and potentially patients to encourage behavioural change.