Background: Overcrowding is an important problem for outpatient services in healthcare facilities. Patient flow analysis (PFA) is a useful method for identifying inefficiencies in and facilitating patient flow. Objective: PFA was used to estimate patient wait time and determine how different clinical disciplines impact wait times in the studied hospital. Methods: This cross-sectional study investigated a study population comprised of outpatients who referred to clinics at a general hospital in Tehran, Iran. A total of 3836 samples were selected from different stations. Nonrandomized quota sampling was used, and data was gathered using workflow checklists, the content validity of which was proven by experts and hospital authorities. SPSS statistical software was used for data analysis. Results: Total patient stay in the outpatient setting was an estimated 77 minutes (without considering para-clinic units and pharmacy). More than 90% of this time was spent waiting. The wait time of patients at the clinic was greater than that at other stations, and it was less at the cash station than at other stations. Wait times varied at different clinics (P value < 0.001) and were correlated with physician delay (P value < 0.001). Conclusion: The most important result of using PFA in the outpatient setting was managing wait times. This study indicated that a considerable amount of a patient’s total stay in the system was related to waiting for physical examinations. This suggests that the first priority in improving the system should be managing patient wait times for physical examinations.