Introduction: Ghana has adopted and implemented Intermittent Preventive Treatment using Sulfadoxine-Pyrimethamine (IPTp-SP) and Insecticide Treated Nets (ITNs) in an antenatal care (ANC) context to prevent malaria among pregnant women. However, the increased ANC attendance, and its frequency facilitated by a free maternal health care policy in Ghana does not correspond with the uptake of IPTp-SP and ITN use among pregnant women. This study sought to identify the health system factors affecting the delivery of IPTp-SP and ITN to prevent malaria among pregnant women in Ghana. Methods: A qualitative study was conducted across four levels of the health system, that is health facilities, district and regional health directorates and the national level, National Malaria Control Programme (NMCP). Audio recorded key informant interviews were conducted with purposively sampled health workers and managers across the various levels, after which they were transcribed and imported to NVivo for analysis. Using the World Health Organization’s (WHO) Health Systems Framework as the theoretical basis, thematic analysis was conducted under broad themes of the building blocks. Findings are presented in narrative quotes, with a MindMap used to summarize the various health system factors and their interrelated relationship influencing the delivery of IPTp-SP and ITN.Results: Health system factors identified included health staff untrained on malaria delivery directives due to an ineffective trainer of trainer (ToT) system. Additionally, health worker confusion on when to commence SP (at quickening or ≥16 weeks) was found to result in delayed start of SP. Stock outs in facilities due to procurement delays at the national level resulted in missed opportunities to deliver SP to eligible pregnant women at the ANC. Similarly, ITN stock outs led to eligible pregnant women not receiving one at ANC clinics. Conclusion: Poor health worker knowledge on policy directives, a consequence of ineffective training strategy led to delayed delivery of IPTp-SP to eligible pregnant women. Supply chain management challenges related to stock of SP and ITN resulted in missed opportunities to deliver the interventions to pregnant women attending ANC.