(1) Background: To assess whether the start time influences the outcomes of esophagogastroduodenoscopy (EGD). (2) Methods: We retrospectively analyzed the clinical data of patients who underwent EGD between January 2021 and December 2021 in our endoscopy center. The EGD were divided into three shifts, according to the start time. The lesion detection rate (LDR) and endoscopy biopsy rate (EBR) were used to evaluate the quality of the EGD. (3) Results: A total of 14,597 procedures were included in this study. The LDR of shift 2 was significantly lower than that of shift 1 (62.4% vs. 58.5%; < 0.001). The EBR of shift 1 (37.4% vs. 31.5%; < 0.001) and shift 3 (35.5% vs. 31.5%; = 0.024) were significantly higher than that of shift 2; the EBR in shift 1 did not differ significantly from shift 3 ( = 0.280). The multivariable analysis for the EGD performed before 14:00 demonstrated a graded decrease in the LDR and EBR after adjusting the confounders ( < 0.001). (4) Conclusion: In a continuous working period, the lesion detection and biopsy submission of EGD are superior to those in the first three hours compared to the last three hours; the LDR and EBR decreased as the day progressed, probably due to the endoscopists' fatigue.