The pharmaceutical industry is key to the survival of the human race, but equally becoming increasingly susceptible to global disruptions. In Nigeria, records have shown that the industry is plagued with several problems, inclusive of low employee productivity, poor market share, low innovation performance, poor and marginal sales growth and low profitability, which are likely a result of a lack of strategic flexibility in the face of increasing environment turbulence and intense competition. Despite efforts from researchers, the moderating role of supply chain agility has been largely overlooked in the literature. Therefore, this study examines the moderating role of supply chain agility on the relationship between strategic flexibility (resource flexibility, coordination flexibility, proactive flexibility, reactive flexibility and futurity) and organisational performance. A survey research design was used to collect data from 642 management and senior staff employees of six pharmaceutical companies listed on the Nigerian Exchange Group. A total enumeration method was adopted for the study, with a well-structured adapted questionnaire, having Cronbach’s alpha reliability coefficients ranging from 0.725 to 0.945. Partial Least Squares Structural Equation Modeling (PLS-SEM) was chosen to achieve the research goal. The PLS-SEM analysis revealed that strategic flexibility positively affects organizational performance (β = -0.093, p> 0.050, Q2 = 0.644). However, supply chain agility negatively moderates this effect, indicating that while agility is beneficial independently, it can counteract the positive impact of strategic flexibility when combined. The study recommended that the management of pharmaceutical companies in Nigeria should pay serious attention to strategic flexibility as an organizational capability that can enhance performance in the face of increasing uncertainties in and unpredictability nature of the business environment.