Background Patient flow describes the progression of patients along a pathway of care such as the journey from hospital inpatient admission to discharge. Poor patient flow has detrimental effects on health outcomes, patient satisfaction and hospital revenue. There has been an increasing adoption of health information systems (HISs) in various healthcare settings to address patient flow issues, yet there remains limited evidence of their overall impacts. Objective To systematically review evidence on the impacts of HISs on patient flow management including what HISs have been used, their application scope, features, and what aspects of patient flow are affected by the HIS adoption. Methods A systematic search for English-language, peer-review literature indexed in MEDLINE and EMBASE, CINAHL, INSPEC, and ACM Digital Library from the earliest date available to February 2022 was conducted. Two authors independently scanned the search results for eligible publications, and reporting followed the PRISMA guidelines. Eligibility criteria included studies that reported impacts of HIS on patient flow outcomes. Information on the study design, type of HIS, key features and impacts was extracted and analysed using an analytical framework which was based on domain-expert opinions and literature review. Results Overall, 5996 titles were identified, with 44 eligible studies, across 17 types of HIS. 22 studies (50%) focused on patient flow in the department level such as emergency department while 18 studies (41%) focused on hospital-wide level and four studies (9%) investigated network-wide HIS. Process outcomes with time-related measures such as ‘length of stay’ and ‘waiting time’ were investigated in most of the studies. In addition, HISs were found to address flow problems by identifying blockages, streamlining care processes and improving care coordination. Conclusion HIS affected various aspects of patient flow at different levels of care; however, how and why they delivered the impacts require further research.