Performance appraisal is the process of assessment of an individual performance, against factors like job knowledge, quality and quantity of output, initiative, leadership abilities, supervision, dependability, cooperation, judgment, versatility etc. In spite of its widespread use, plethora of benefits, the practice of formal performance appraisal continues to come under considerable inquiry, dissatisfaction and criticism, which may lead to many major problems out of which one is decrease in the employee retention (major problem of Indian pharma industry). Out of many factors which may make performance appraisal ineffective, most important is lack of efficient and accurate ways to evaluate performance with perceived fairness among employees. This study has been conducted with an objective to evaluate apparent fairness in presently "practiced performance appraisal system" in selected pharmaceutical organization and to assess the level of its "effectiveness" or "level of satisfaction" from the employee perspective by utilizing organizational justice models. The data were collected from the two pharmaceutical companies situated in Madhya Pradesh, which was statistically analyzed and were subjected to mean score calculations followed by rank order and factor score. Respondents from company A perceived that performance appraisal system was effective as indicated by their agreement with 7 of the 9 scales. Whereas respondents from company B indicated neutral with 5 of the 9 scales measuring reactions to agreement with PAS effectiveness. By cross-sectional study it was observed that in Company A & B overall has no significant difference in employee performance appraisal effectiveness based on job grade, experience in current job, age, gender wise and level of education. But significant difference in opinion has been observed only in respondents of Company A with supervisory and non supervisory responsibility as compared to Company B. Overall by the data obtained it was concluded that 74.83% of company A and only 54.87% of company B employees consider PAS fair and effective. Hence are satisfied with their presently practiced Performance Appraisal System.