The study investigated the effect of e-Performance Appraisal on Employee Performance in the Presidential Amnesty Programme Office, Abuja, Nigeria. The objective of the study is to specifically assess the effect of the proxies of e-Performance Appraisal viz. goal setting, e-performance review and feedback on employee performance. The study made use of a survey research design; where primary data were collected from a census sample of 122 management and operational level employees in the Presidential Amnesty Programme Office in Abuja. All the questionnaire issued was completed and returned representing a 100% response rate. The questionnaires contained closed-ended questions that were rated on a Likert-5-point Scale of ?Strongly Agree, Agree, Undecided, Strongly Disagree and Disagree.? The data was then analysed with the Multiple Linear Regression. Arising from the result, the model was significant at 0.000 and the null hypothesis was rejected. It was concluded that the employee performance Presidential Amnesty Programme Office in Abuja is affected by e-Performance Appraisal, however, of the proxies tested, e-Performance Review is insignificant, while Goal Setting and Feedback are significant. The study recommends that organisations that seek to increase their employee performance should shift from the traditional performance appraisal system to the e-Performance Appraisal system. This is because e-Performance Appraisal has a positive effect on employee performance.