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Managing the performance of civil servants is critical as they are responsible for providing public services and promoting public welfare. One way of understanding the effectiveness of a Performance Appraisal System is to measure it against the reactions of the employees. These reactions have shown to be positively related with the overall outcome of performance appraisal. ‘Perception of Fairness’ is one such reaction and this study attempts to explore and discuss different factors that are associated with such fairness perceptions. Using a Mixed Methods approach, quantitative and qualitative data were collected through a survey that investigated the perceptions about six different factors (Performance Appraisal Instrument Design, Performance Appraisal Process, Uses of Performance Appraisal, Organizational Politics, Employees Attitudes towards Performance Appraisal and Ratee-Rater Relationship) and the Fairness of Performance Appraisal System. Responses from 130 civil service officers from BPS 17-19 were analyzed. The empirical findings confirmed that the factors were significantly associated with the perceptions of fairness while the qualitative responses helped identify major issues in the current Performance Appraisal System in the Federal Civil Services of Pakistan