This was a questionnaire-based cross-sectional study that explored the impact of the COVID-19 pandemic on the availability of essential medicine and personal protective equipment (PPE) in Saudi Arabia. Purposive sampling technique was used to recruit individuals working in the supply chain departments in different healthcare sectors in Saudi Arabia. One hundred and three pharmaceutical and medical supply chain employees participated in the study. Most of the participants (58.3%) were aged ≥35 years, male (65%), and pharmacists (92.2%). The majority of participants had at least two years of experience in supply chain (77.6%), worked in public hospitals (95.15%), and were mostly working at healthcare institutions located in Riyadh province (59.2%). Approximately 51% of the participants reported shortages of 10 or more essential drugs. Tocilizumab, hydroxychloroquine, lopinavir/ritonavir, ribavirin, dexamethasone, enoxaparin, interferon beta-1b, cisatracurium besylate, prednisolone, hydrocortisone, methimazole, and methylprednisolone were reported to be in shortage by at least 8% of the participants. Almost 70% of the participants reported that the pandemic did not significantly impact the prices of prescription drugs in shortage (e.g., ≥25%). Moreover, about 70% of the participants reported direct purchasing or procurement of drugs in shortage. Surgical masks, face shields, medical gowns, and N95 respirators were reported to be in short supply by 33% or more of the participants. Approximately 53% of the participants reported the prices of PPE in shortage had seen an increase by at least 25% during the pandemic. Although the COVID-19 pandemic has caused a significant disruption in the global pharmaceutical supply chain, its impact was largely manageable in Saudi healthcare institutions. This can be attributable to multiple reasons such as the effective exchange programs between hospitals and the drastic increase in public healthcare spending to ameliorate the negative impact of the pandemic on the healthcare sector.