This study aimed to assess the application of electronic governance systems and their influence on the governance of public secondary schools in Meru district. The following were the objectives: determine the extent of applicability of electronic governance systems in school management and their influence on the management of public secondary schools, and to investigate the challenges faced by heads of schools in executing electronic governance systems. Theory of acceptance and use of technology developed by Venkatesh guided the study. Convergent mixed design was adopted, targeting 72 participants, including 44 school heads, 26 WEOs, DSEO and DITO. Purposive sampling was used to select the participants. Questionnaires, observation checklists, and interview guides used to collect data were validated through the use of experts. Cronbach alpha was used to estimate the reliability of instruments yielding satisfactory results of HoSQ =0.78 and WEOsQ = 0.82. Qualitative data underwent thematic analysis coding to identify patterns and themesData were analyzed using tables, frequencies, percentages, mean scores, and thematic coding. The findings indicated a positive trend in the application of electronic governance systems in public secondary schools’ management. In conclusion, despite the challenges, electronic governance systems are still applied in the management of public secondary schools in Meru district. Recommendations were made for heads of schools to address the identified challenges, for ward education officers to provide support and guidance, and for policy makers and the Ministry of Education, Science and Technology to formulate policies and allocate resources to promote the application of electronic governance systems in schools.