The study focused on the factors affecting internal auditors ‘performance in public universities in Kenya. It aimed at achieving the objectives: to determine how the working environment, to assess how the challenges to the independence of internal auditors, to assess the impact of the level of technical competency affects the performance of internal auditors in public universities in Kenya. Thus this study evaluates the effect of working environment,establishes the effect of internal auditor’s independence and the effect of internal auditors competence on the performance of internal auditor in public universities in Kenya. Descriptive research design was applied, with a target population of the chief internal auditors from 31 chartered public universities in Kenya which are registered by the Higher Education ministry. A random simple sampling technique was applied o give the sample size of 31. Primary data was used for analysis. The study found out that the internal auditors working environment, internal audit independence and authority, internal auditor’s technical competence impacted on the performance of internal audit function.The study recommended that auditors should consider complying with professional standards as the most important contributorto internal auditing performance. The management in the public universities should keep organizing seminars and workshops where the internal auditors would be trained frequently by experts either internally or externally.