Studies on private universities in Kenya show that they face challenges that negatively influence performance. These challenges may require redesigning human resource management practices and innovative strategies to improve performance. Despite several studies on practices of human resource management and performance, research on the joint effects of selected variables on employee performance is rare. The study objective was to examine the joint effect of human resource management practices, innovation, and organizational size on employee performance. This study was guided by human capital theory, goal-setting theory, and innovation theory as a foundation. The research had cognizance of the positivist philosophical paradigm. It applied a descriptive cross-sectional survey research design to collect data. The target population was 2826 regular academic staff from 36 private universities. The self-administered questionnaires were used to collect primary data. Multiple regression was used to test the null hypothesis. The results established that the joint effect of human resources management practices, innovation and organizational size on employee performance was positive and statistically significant. Individually, innovation and organizational size may increase or reduce the predictive power of independent variables on employee performance. The results reject the null hypothesis. This study contributes to theory development, policy, and management style for policymakers in Kenyan private universities. The outcome of the study will help educational managers in formulating human resource policies and strategies that enhance innovation. The study recommends an adequate budget for human resource information systems and emerging technologies as enablers of innovation. It also recommends an assessment of the institutional environment for innovation and regular faculty high performance. It is recommended that similar studies be conducted at universities in Kenya and that longitudinal studies be conducted for future direction.