Background and Aim: Decision-making as an important managerial function means choosing the best option out of available alternatives for solving a problem. Female Managers face several challenges in decision-making in healthcare organizations. The study aimed to explore women managers’ challenges in decision-making in healthcare organizations. Materials and Methods: A qualitative approach was used in this study. In-depth semi-structured interviews were conducted with 23 women managers in Tehran healthcare organizations. The participants were selected using purposive and snowball sampling techniques. The qualitative data was analyzed using thematic analysis method. Results: Twenty-two decision making challenges were identified and grouped into 5 categories. These challenges include structural challenges (i. e., mission and type of functions, organization size, workload, resource scarsity, and law and regulation limitations), procedural challenges (i. e., weakness in defining the problem, wrong goal setting, and lack of criteria for choosing the best solution), human challenges (i. e., staff shortages, and their low motivation, knowledge and skills), cultural challenges (i. e., personal belifs, personal profit seeking, indifferences and gender stereotyping), and managerial challenges (i. e., emotions, insufficient authorities and lack of top managers’ support). Female managers used solutions such as using evidences, group decision making, problem prioritizing, effective internal and external communication, transparency, systems approach, employees’ education and training and improving organizational culture to overcome these challenges. Conclusion: Healthcare female managers face several important challenges in decision-making. Appropriate measures should be taken to reduce these challenges to achieve better results.