Abstract: Accounting systems is a system that records and process data of transaction and events into meaningful information for use in planning, controlling and operation of business. The purpose of this study was to establish the effect of accounting systems on performance of Public Universities in Kenya. The study adopted descriptive research design using a case of one public University in Kenya. The study targeted all the 106 staff working in the Administration and Finance division of Egerton University. Simple random sampling technique was used to select 83 respondents out of which 79 respondents participated in the study. Data was collected using self-administered questionnaire. Quantitative data collected were analyzed using descriptive statistics . Simple regression model was also used to analyse the results. The study established that there was statistically significant relationship between Accounting systems and the performance of university. The study recommends that the management of university should consider and improve on their Accounting systems to enhance accuracy of accounting reports, customer satisfaction, management accountability and transparency, since they significantly affected their performance. The study also recommended that the same study be carried out in Finance and Microfinance institutions, private and other public sectors to find out if the same results would be obtained.