BACKGROUND: Maternal and neonatal mortality is a global issue acknowledged by the Sustainable Development Goals (SDGs). Adequate ante-natal care (ANC) is pivotal to reducing these mortality rates, while understanding why women don't attend ANC is crucial to addressing the SDGs. AIMS: Using routine primary health care data to determine the factors associated with inadequate attendance by Palestine refugees (PR) to ANC seeking facilities provided by the United Nations Relief and Works agency for Palestine Refugees in the Near East (UNRWA), Jordan. METHODS: A backwards logistic regression model incorporating non-health system factors and health system factors, was performed using UNRWA data. RESULTS: A younger age of women was associated with inadequate ANC visits (P = 0.0009) in the non-health systems model. For health system factors, pregnancy risk status, having a gynaecologist review and the health centre attended were factors found to be significantly associated with ANC attendance (P < 0.0001). CONCLUSIONS: Understanding the health system factors associated with ANC attendance can lead to changes and improvements in UNRWA's operational policies.