During the COVID-19 pandemic, the number of visits in emergency departments (ED) worldwide decreased significantly based on several studies. This study aims to compare the patient flow in the emergency surgery department during the COVID-19 pandemic and a control period in the emergency department of a public tertiary care hospital in Greece. The overall patient flow reduction regarding the ED visits between the two examined periods was 49.07%. The emergency surgery department’s corresponding visits were 235 and 552, respectively, which indicated an overall patient flow decrease of 57.43%. Chi-square analysis showed that age groups and ambulance use had statistically significant associations with the periods examined. An independent samples t-test was applied and deduced that the average patient’s age was statistically significantly higher in the COVID-19 pandemic than in the non-pandemic period. By analyzing hospital information system data, useful conclusions can be drawn to prepare a surgical emergency unit better and optimize resource allocation in a healthcare facility in similar critical situations.