This research was inspired by the rules of the Financial Services Authority (FSA) in Indonesia regarding the necessity for good corporate governance for rural banks (RB). So far, good corporate governance regulations have only been binding on commercial banks, but with the development and expansion of services and increased business volume of rural banks, the risk of rural banks has also increased, so this has encouraged the need for good corporate governance in rural banks. To achieve the application of good corporate governance, the quality of a management accounting information system (MAIS) is needed which is supported by the effectiveness of internal controls and manager’s competency. The method used is the explanatory survey method. The sample technique uses random sampling from the target population of the study—as many as 54 rural banks in the North Sumatra Province of Indonesia with a total sample of 45 rural banks. Respondents who are targeted are parties related to management accounting information systems, namely the board of directors or operational managers. Data obtained directly through research questionnaires were processed using Statistical Product and Service Solutions (SPSS) applications. This study found that the competencies of managers affect the quality of MAIS in rural banks, while the effectiveness of internal controls has no effect. This study also found that manager’s competency and the effectiveness of internal controls had an effect on the application of the principles of good corporate governance in rural banks if mediated by the quality of MAIS.