Researchers sought to see how inconsistent Optical Coherence Tomography (OCT) scan location affected glaucoma progression detection using GPA for a study. A total of 84 glaucomatous eyes with at least 4 serial OCT tests were included in the study. An analysis was performed without manipulation (control set). After the OCT scan of the most recent test was intentionally moved inferotemporal to evaluate the OCT Guided Progression Analysis (GPA) ability to adjust the OCT scan location (test set). The eyes were divided into adjustment and nonadjustment groups based on the superior and inferior quadrant retinal nerve fiber layer (RNFL) thickness agreement between the control and test sets. When the OCT GPA parameters of the control and test sets were compared, the test set had a greater superior RNFL thickness and a lower inferior RNFL thickness (P<0.05). In addition, the eyes in the nonadjustment group (n=21, 25%) had a lower chance of using the eye-tracking function (P=0.003) and a higher frequency of using the “R1” registration method of OCT GPA (P<0.001) than the eyes in the adjustment group (n=63, 75%); all eyes using the “R1” method were in the nonadjustment group, and all eyes using the “R2” method were in the adjustment group. Inconsistent OCT scan location caused changes in RNFL thickness that were not completely compensated even when OCT GPA was used, especially when the “R1” registration method was used. These findings suggested that glaucoma progression may be misdiagnosed.