Service quality is a key antecedent to customer satisfaction and that quality service is considered as an essential strategy for success and survival in today’s competition (Wirtz, 2008). Internal Quality Assurance emphasizes the development of each institution’s statements of expected outcomes and its own means of gathering evidence of their achievement. The main objective of the study was to analyze the influence of quality management system practices on performance of selected private universities in Kenya. The study adopted system theory, total quality management theory, balance Score Card theory and Strategic Clock Model as the main theories and models of the study. The study targeted 18 Chattered Private Universities in Kenya. People to be targeted will be 245 Deans and Employees Working in Quality Assurance Departments of the 18 Chartered Private Universities in Kenya and 170 third and fourth year students in the 17 Chattered Universities. Further, the study will apply sampling formula by Yamane (1967) to arrive at the 153 Deans and Employees Working in Quality Assurance Departments a sample size appropriate for the study. The number of students was arrived at through cluster sampling. Both the students and university employees will be subjected to questionnaires and interview guides. Descriptive statistics was used to analyze the data collected. Closed questions will be analyzed through the help of the Statistical Package for Social Sciences (SPSS) computer software by assigning numbers to responses for analysis of qualitative data, as it is efficient. Open ended questions were analyzed through percentages, frequencies, tables and bar graphs. The inferential statistical method used in the study was simple linear regression and multiple regression analyses. The study established that quality management system influenced performance of private universities in Kenya.