Vietnam is facing a problem of over-crowding in public hospitals. Long waiting time is a major dissatisfaction for patients. Reducing waiting time benefits not only patients but also hospitals in decreasing overall workload. To identify factors contributing to long waiting time in outpatient clinics, a cross-sectional study was conducted at a national hospital in Vietnam. The time for each process of 7,931 patients who visited the outpatient clinics within Thong Nhat Hospital from 5 to 9 September 2016 was collected from the computerized clinical database. Characteristics of patients (age, sex, address, day of visit, registration time, visited department and test) and waiting times were studied at the outcome measures. Multivariate analyses using the linear regression model was carried out to evaluate the contribution of these factors to the total waiting time. Among 7,931 patients, 52.3% were women, 46.3% were 60–80 years, and 64.8% registered between 5:30 and 9:30. The mean total waiting time was 104.1 minutes. The analysis on total waiting time among 4,564 patients who visited one department without any test showed that department group and registration time were significantly associated with a total waiting time. In 1,259 patients who visited one department with one test, early registration and undergoing blood tests were significantly associated with a longer total waiting time. These results showed that old age, visiting internal medicine departments, early registration time, and undergoing blood tests were factors contributing to a longer total waiting time in the outpatient clinics within Thong Nhat Hospital.