Information technology (IT) has dramatically transformed business processes in many industries including healthcare, where electronic health records, electronic prescribing and computerized provider order entry systems have positively changed the practice of healthcare. Recently, King Faisal Specialist Hospital and Research Center, Saudi Arabia, implemented various IT systems in multiple clinical and administrative departments leading to major transformation in healthcare workflows and business processes. At the pharmacy department, many Healthcare-IT alignment challenges are still perceived. Information about challenges of strategic alignment were gathered using qualitative survey methods, through conducting semi-structures interviews, to collect opinions, experiences and suggestions. Findings were first validated, according to published literature and research work, then sorted into fourteen challenges categorized into four main areas and recommended solutions: 1) Improving organizational communication, 2) Enhancing organizational governance, 3) Specifying the alignment scope and building the architecture and 4) Developing organizational and human skills.