To develop a reliable and efficient method for quantifying the area of preserved retinal pigment epithelium (RPE), facilitating the evaluation of disease progression or response to therapy in choroideremia (CHM). Methods: The fundus autofluorescence images of CHM patients were captured at baseline and 1 year. A Photoshop-based method was developed to allow the reliable measurement of the RPE area. The results were compared with measurements generated by the Heidelberg Eye Explorer 2 (HEYEX2). The areas measured by two independent graders were compared to assess the test-retest reliability. Results: By using the Photoshop-based method, the area of the RPE measured from 64 eyes was seen to decrease significantly (P < 0.001) at a rate of 2.57 ± 3.22 mm 2 annually, and a percentage of 8.39% ± 5.24%. The average standard deviations for Photoshop were less than that for HEYEX2 (0.5-1.1 in grader 1; 0.4-1.6 in grader 2), indicating less intragrader variability. The RPE decrease as determined by the Photoshop-based method showed excellent reliability with an intraclass correlation coefficient of 0.944 (95% confidence interval, 0.907-0.966). In Bland-Altman plots, the Photoshop method also exhibited better intergrader agreement. Conclusions: Photoshop-based quantification of preserved RPE area in patients with CHM is feasible and has better test-retest reliability compared with the HEYEX2 method. Translational Relevance: An accurate quantification method for longitudinal RPE change in CHM patients is an important tool for the evaluation of efficacy in any therapeutic trials.