Performance is one of the most important issues for any company, it considered as essential criteria to evaluate companies’ ability to survive in the market or go out of it, especially in the context of a dynamic business environment which is characterized by uncertainty and is full of both changes and challenges, where companies are increasingly facing uncertain situations, and thus companies must find a way that enables them to deal with market fluctuations. Flexibility considered an essential organizational capability that enables companies to get a competitive advantage and reach a high level of performance, especially in an unstable business environment. The dissertation aims to highlight the interaction between strategic flexibility and operational flexibility and how they can affect companies’ performance and considers environmental uncertainty as a moderator in understanding the moderating effect of uncertainty on the relationship between flexibility and companies’ performance. This study is both causal and quantitative and has a structure based on specific steps. The study was carried out in normal conditions in the natural business environment, it carried out at small and medium-sized pharmaceutical companies in Iran. The study is a cross-sectional one, which means the study was carried out at a specific time (2019) and it does not cover a time series. Primary data collected by using an adopted questionnaire, the questionnaires were forwarded to the target population, and responses were then received in the normal way, a purposive (selective) sampling technique was used to collect the data, the total number of responses that were valid for statistical analysis was 228. The response rate was 67.25%. SPSS 23 was used for statistical analysis (reliability test, descriptive analysis, correlation analysis, linear regression analysis, and moderation analysis by using Hayes, 2013). The results showed, both strategic and operational flexibility positively affect companies’ performance. Uncertainty moderates the relationship between strategic flexibility and companies’ performance, but it doesn’t moderate the relationship between operational flexibility and companies’ performance. For more details, resource flexibility positively affects the performance of the companies, and it has the highest impact on the performance of 41.8%. Product development flexibility positively affects the performance of the companies, it ranks second in terms of impact on the performance of 40.20%. Volume flexibility positively affects the performance of the companies, it ranks third in terms of impact on the performance of 31.3%. Coordination flexibility positively affects the performance of the companies, and it has the lowest impact on the performance of 25.3%. Mix flexibility does not affect the performance of the companies.